Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_029356
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: 104744
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:18158 original size:21 final size:22
Alignment explanation
Indices: 18123--18165 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
18113 CTTTCTGTAG
* *
18123 TGTACTTTGTTTTTTATTATTT
1 TGTACATTGTTTTTTATCATTT
18145 TGTACATT-TTTTTTATCATTT
1 TGTACATTGTTTTTTATCATTT
18166 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 17623 -- 18122
TCGCCGAAGGCCGAAGAAGAGAAGCCTTCGGCCCTCATTTTTTTGTTTCAATTTTGAGTTTTTTT
ATCTTGTATTCTTTTCTTCTTTAAAGCAAAATCCTAAAAACAAATAGAGCAGATGGTCCAACTAC
AGAACTTTTTTTTTTTTCTTATGTTTATGGTTGTGCTTTGTGGTACGGCAGCACCCATACTATTT
CAATGGTTGGTAAGTAGAGATGTTCCCACAGGTGCTCCTTTTTCTCATGGTACTATAATACCTAT
TTTTACCTCTTTATTATTGCTTCTAGTTCATGTACATTCCAGGGGATTCATACGCTCTATGGAGA
AAACAGAAAGGATAGTTTTGGTAAAAGCAAAACGCATTTTATTACTCAACATAATTGAAAAAAGC
TCCCCAAAAACTAGAGCTAAAAATGCATTTTTTTTCTTCTTTTTTTTTTTTTCGAATTTTTTTAT
TTTTAAATTTATGGGAGACTTGTCATATTTAGAATCTTTCTGTAG
Right flanking sequence: Indices 18166 -- 18665
AAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGAAAAGAAAACC
GCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAAAAGAAACAAA
GAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAAAATATTTTTGATT
TATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAAGCAAAATTTTGGCTTTTTATTC
TCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGATTTTTTATTG
TTCGCGCCTTACCGAAAAGACTGATGGATGTTGGTCATGACTTTCGAAAAGTTCCCATGACTATG
AAAATTTCACATGGAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGC
CTATGCGCGACCATCTCGTGTTTAAGCTCACGCCATGTGGGCGTG
Found at i:18568 original size:19 final size:20
Alignment explanation
Indices: 18526--18568 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18516 GGATGTTGGT
* *
18526 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18546 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18565 CATG
1 CATG
18569 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 18026 -- 18525
GAGCTAAAAATGCATTTTTTTTCTTCTTTTTTTTTTTTTCGAATTTTTTTATTTTTAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTAGTGTACTTTGTTTTTTATTATTTTGTACATTTTT
TTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGA
AAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAA
AAGAAACAAAGAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAAGCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 18569 -- 19068
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCCTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCTCAAATTAGTGCAAG
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAAAAAGGCCGCGGGTAACGCTAGTTGGCAAAA
TGGCGTTAAGCATTCCTAACAATACGGAAAAAGAGGTCGTGATGATATTCATCTACGTTCGTACT
GTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAGT
TCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAAC
Found at i:41363 original size:81 final size:81
Alignment explanation
Indices: 41228--41377 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
41218 AAAATACTCG
*
41228 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41293 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41309 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41373 CCAAG
65 CCAAG
41378 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 40728 -- 41227
CAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTGGAAATAACATC
AGTATTTCAACAACTTTTTGAGCTCATTTTTCACCCATATAATTCTTTATGTTTTTGTTTGAACA
AGCCAATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGG
ATAACCACTTAGTAACTAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTAACAG
AACTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTAATATTTTGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTTCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41378 -- 41877
TGAGCTTAAGGAAACGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCTAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCGTTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTCATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTGTATTTAGAACTAAAAGAAAA
TAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATAGAATATAGTAGAAAATAATAAGTTGGCGAGGAAGTAAAAATATATA
TATATATCTATAGATATATATATATTTTTTTTTTATTCTGTGGAT
Found at i:48773 original size:16 final size:17
Alignment explanation
Indices: 48752--48789 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
48742 TAATAAATCG
*
48752 AAAAAG-AGAAAATGAA
1 AAAAAGCAGAAAACGAA
*
48768 AAAAAGCATAAAACGAA
1 AAAAAGCAGAAAACGAA
48785 AAAAA
1 AAAAA
48790 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 48252 -- 48751
CACATTTCGAAAATTAGCCAAGCAGATAAGTAAACTTCAAAGTGGTTTTGTTTATCATTATGCTT
TTGTAATGTTGATTGGCTTAACCATATTTATTACCATAATAGGTCTGTGGGATTTTATTTCTTTT
TGGGTAGATAATCGATTGTATTTTATTTACATAGTGAGTTTTCTATTTATTCATTTTGAAAACGA
CATTAGCACGAGCTAAAGGGGGCATACTTCCTTATATAATACCATGAAACTTTAAGGGACGCAAT
GATAAGCCAGTGCTACGCCCTTTTTTCGGCTTCGCTGAGAGGGAGGGCTGAGGCCCGACGAAGCC
TAACAAGCAAAAAAAATAGATTTTTTGGAGCCTAAGCTATGCTCTGCGGTCTAGCTACGATAAAT
CGTAAAAAAAAATGGGTCCTCGAATAAAGCACGTTATTGCCTTGGGTCTATGAGGAATCTGAAAA
AGAAGAAGAAAAAAGTAAAGGTTGGAATGATAGAATAATAAATCG
Right flanking sequence: Indices 48790 -- 49289
AATTTTTCGGCTTTTTTTATCCTCCTCGATCGTGACTGAGGCCGTCTGGTCATAATAGCAAGCCC
TAAAGCATTGAACAAAGCGGCAAAAGACGAAGCATGCAATTACATAGTATGCGCGTATAAAAGCT
CATCAAGTTATGCAATTATTGCGGGCTTTATAGAAGTGCAGGGGGTTATGATGATATACCCATAA
GGCCTCTATGGCTGGAAAGCCGAGAAGAAATGTGGACCCGCGGCCTGCGAAGAGAGCTGCGTCCC
CGGGATCTTTTGGAAAAAGAGTAAACATTTATGTTACAATTTTTAGCTCCATTTTATTCCAATCT
CAGTGGTCTTATTCTGTGTCCTTTGTTAGGAAGCATTATTCTTTTTGTTATCCCTAATCCCAGAA
TACGACTGATACAAAGTATTGGTTTGTGCACCTCTTTGATTACTTTTCTATATTCCCTTTTTTTT
TGGATACAATTCGATAATTCTACAGCCAAATTTCAATTCGTGGAA
Found at i:63250 original size:14 final size:14
Alignment explanation
Indices: 63231--63258 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63221 TCTTTGTTTT
63231 TATAAGATATGAAG
1 TATAAGATATGAAG
63245 TATAAGATATGAAG
1 TATAAGATATGAAG
63259 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 62731 -- 63230
AGAGGCTGTTAAGATAGCTGCTAATGCCATAGGCGCGTTTACTGCGGCGGGGTACTTGGTTGTAC
GTGCACAATTTAAATAGAGCGAATGCATTAGAATTGTAAGAAAAAAGCCTAAAATTGAAAAAGCT
AAAGTTCAATTATAAGGTACTTATTAATGAAGCTAAAAACACGGATCAGCTTTTGGAAGAAATTG
AAGAGCGTTAAATGAAAGAAATTAAGGCTTGTTGGTTGGGTAGTAAAAAAAATGAGTACTGATGA
AGAATGAACAGCCACGTCTAGATGATGCTGTTTAGCGTGTAGTAGAAGCTAAATACAACAAGCTG
CAAGCTAAGGGTAAGGGTCTTCGCGCGACAAGATTCGAGATCAGTATGCGGAACAAACGACCATA
AAAGAAAGGCCACGAGTATCATAGGCAGACCTTCAACAGGCACCTAAAAAAAAATTACCACCTAA
ATTATCTATTAAGTACCCTGTCCCAAACGCAAACTTCTTTGTTTT
Right flanking sequence: Indices 63259 -- 63758
GTATTTTTGTTTCTCGAAGAGCCATCGGGAACTTAGGTTCTTTTATTTATCGAGTTTCGCAAGTA
TATCTTTCTTAGGATCTAAATCCTATTAATTTGAACGTAGAGTTGTATGATGCGAAACTATCACT
TACGGGGTGGGTTTAATCTTAGATTTTTTTATTTTCTGAGTTTTTATGGGATTATTATCGCGGGT
TTGTCTATCCTAATGGGCGTCTAACAAAAAAATTGATTTTTTTGTTGGTTGGCCCTTTTGTGGGG
CCTGTTGAAGGGCCGAAGTAGTTCTGAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACA
TGGCTATTTCCAATTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGC
AACACCTATGATGCAAGGAATAATTGAGTGCGCCTAGATATATCATCACGGTTGCAGAGCTCTGC
TCCAACTCTGCCATATCTGCTCGAGCTGGCTATCGCCAGGATGTG
Found at i:104606 original size:10 final size:10
Alignment explanation
Indices: 104591--104616 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
104581 TCTTCTTATA
104591 AATAATCTTT
1 AATAATCTTT
104601 AATAATCTTT
1 AATAATCTTT
104611 AATAAT
1 AATAAT
104617 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 104091 -- 104590
TCTATCGGGGGGGGGGGAGTTGTGCATCATAGGTACCTTCTTATTGCTGCGAAGGGCGATATGAA
AATAACCCCCCTATCCAACCTCATTCTGTTGCGCGAAATCCATCATTGGCTAAGCAATTATTTGG
TTATGCCATCTTAGGTTTCGCTTTAACAGAAGCTATTGCTTTGTTTGCCTTAATGATGGCCTTTT
TGATCTTATTTGTTTTTTAATTTTTTGGTGCTGCGATTTTTTGGGAAAAAAACTATATTTTGGCC
GCACCCTATTGGCTTTGCGAATAGGGCTGCGCCCAAAAAATCTAGATTTTTTGGCACCTTAGGGC
CGAACGATTAGTACGTTCGAGCCCTTCACCACTTGCTACCAAAAGCATAAGCGTAAAAAAACTGA
ACTGACAAAGATTTTAACCTTAAAGGCTCATTGGATAAAAAAAGAAGCAGGACAAATATATCTAT
ATATATATTTTTTTTTCTTTTTTAGCTGCTTCACTTCTTCTTATA
Right flanking sequence: Indices 104617 -- 104744
GCATAGCTTCGCGTGCTTTTCGATTGATGATGGGACCGAAGACGAAAGGCGCGAAGCGGCCGCGG
GTCTAGATTCTCGTTTTTTCGGCCGCGCGCCTGCGGCGGCCCTCGGTCGTTGTTAACTTACCA
Done.