Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_039775
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: 114831
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:1712 original size:13 final size:13
Alignment explanation
Indices: 1694--1718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1684 AACAATATTG
1694 TACATAATAATAA
1 TACATAATAATAA
1707 TACATAATAATA
1 TACATAATAATA
1719 CATATCGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
TACATAATAATAA
Left flanking sequence: Indices 1194 -- 1693
TTTTGTTGCGCCCTATGTCTTCATGGCTTCAGAGAGCTGACGCCCTTTTATATATTTTTTTTATT
TCTCTTTATTCTTGTGAAAGAAGGCCGCAGGCCTCTAAGCTGGCGATAGTTCAAAATGCCTTATT
GCAAAGAAGACCTCATAAAAAGGGCCTTTGATACAAAAAGAGAAAAGTTAAGTAGGCGTCACCAA
CTTTATCATATCATATAAAGGGGCGTAGCCCTATTACTTTTGTGGGAAATGCCATGTTTCTGTTC
GTTGGCAGTGTTCGTCGGCACTTTTCCGTCTTTGCTGCTCAGTCTAAAGTCGGTGTGAGTGCCTT
CTACACTCGTTTTTGTGCTCCTGGGAAAGTGTGCCTTTCTTTGGCCTGCGAGAGAAGGCTGCGCC
GAAGAAGAAAAGCAGCGCCGAAGGCGCAGCGAGAAGGTAAGAATAAAAAAGGAAATGAATATTCT
GTACTAGCGATAGCATAAATACTATTTACAAAACTAACAATATTG
Right flanking sequence: Indices 1719 -- 2218
CATATCGAAAATATTCCTTTACTTCGGTTCATCAGGAGTCCACGTTAATCCCCAGTCCGAAAGCG
GATTCCCATTATTTTAAAGTTCCGACAGGAATTGCTCTACGCCACCGTCTTAATTAATTTTAATT
AATAGGCGGCCTTCTTACTTTTATTGATTATCGCCAAGCTGCGCCCGACCGTCCGTATAGGACAC
GGCCAAAGCCCAACAAAGAGAGAGAGCTAAAGCCCTGCCTACAGAGAGCGCCTGCTAAAGCCCTT
TGGCCCTACAGAGAGCCTTCGGCCTGCGGCCATTAATATTTTTGTGGAGGAGTATTAGTGAGGGC
CGCAGGCGCTACTGTATACAGTCCACTCGCTGCAATTGTTCAGCCTTCGTCGCCGGCCAAATATA
TTTGTCTTTATAAATATATTTGTTTTTATTTGATGATATTTGTTTCTATTTGATGATATATATAT
GATTGGCAGTTATTTTGGCTATTCCGGGTAGTAATTCTTCCCCGT
Found at i:2125 original size:18 final size:18
Alignment explanation
Indices: 2102--2137 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2092 GTCGCCGGCC
2102 AAATATATTTGTCTTTAT
1 AAATATATTTGTCTTTAT
*
2120 AAATATATTTGTTTTTAT
1 AAATATATTTGTCTTTAT
2138 TTGATGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (18 bp):
AAATATATTTGTCTTTAT
Left flanking sequence: Indices 1602 -- 2101
CGAAGGCGCAGCGAGAAGGTAAGAATAAAAAAGGAAATGAATATTCTGTACTAGCGATAGCATAA
ATACTATTTACAAAACTAACAATATTGTACATAATAATAATACATAATAATACATATCGAAAATA
TTCCTTTACTTCGGTTCATCAGGAGTCCACGTTAATCCCCAGTCCGAAAGCGGATTCCCATTATT
TTAAAGTTCCGACAGGAATTGCTCTACGCCACCGTCTTAATTAATTTTAATTAATAGGCGGCCTT
CTTACTTTTATTGATTATCGCCAAGCTGCGCCCGACCGTCCGTATAGGACACGGCCAAAGCCCAA
CAAAGAGAGAGAGCTAAAGCCCTGCCTACAGAGAGCGCCTGCTAAAGCCCTTTGGCCCTACAGAG
AGCCTTCGGCCTGCGGCCATTAATATTTTTGTGGAGGAGTATTAGTGAGGGCCGCAGGCGCTACT
GTATACAGTCCACTCGCTGCAATTGTTCAGCCTTCGTCGCCGGCC
Right flanking sequence: Indices 2138 -- 2637
TTGATGATATTTGTTTCTATTTGATGATATATATATGATTGGCAGTTATTTTGGCTATTCCGGGT
AGTAATTCTTCCCCGTTTACACAGAAACAAGAAATAAAGAAACAAGAAATAGATTTATTTTATTA
GGCTTGGCAAATTGTAATTAATTGATAAATTGATTACATCAAATTTTTCATAACCTAAAAAAACT
AATTAGGTTATGATTAGTTTTTTTATACTTTGGTGAAGCTGACGCCCTTTGCCATGACCTTTCGG
GGGCGAGGCGGGGCTCCGCCCCCCAATGGACTAGGTCCTTAGAGGGCAGAGCGGGTAAGTGCTTA
AGTGGCACCATCTGCTAAGACGTCTAAATGCTTTCCTTTATAGCCGGAAGTTCTGAGAAGGTATG
AAATGCTGGAGGGCTTTTGACCATCCATTCAAGTGTCGTTGAATTCTGTTCAACAGCCCAAGGAC
TTGGAGCACACTTGTTTTCACTGGTTAACGTAAAAAAAACCACTA
Found at i:2149 original size:20 final size:20
Alignment explanation
Indices: 2124--2167 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2114 CTTTATAAAT
*
2124 ATATTTGTTTTTATTTGATG
1 ATATTTGTTTCTATTTGATG
2144 ATATTTGTTTCTATTTGATG
1 ATATTTGTTTCTATTTGATG
2164 ATAT
1 ATAT
2168 ATATATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.61
Consensus pattern (20 bp):
ATATTTGTTTCTATTTGATG
Left flanking sequence: Indices 1624 -- 2123
GAATAAAAAAGGAAATGAATATTCTGTACTAGCGATAGCATAAATACTATTTACAAAACTAACAA
TATTGTACATAATAATAATACATAATAATACATATCGAAAATATTCCTTTACTTCGGTTCATCAG
GAGTCCACGTTAATCCCCAGTCCGAAAGCGGATTCCCATTATTTTAAAGTTCCGACAGGAATTGC
TCTACGCCACCGTCTTAATTAATTTTAATTAATAGGCGGCCTTCTTACTTTTATTGATTATCGCC
AAGCTGCGCCCGACCGTCCGTATAGGACACGGCCAAAGCCCAACAAAGAGAGAGAGCTAAAGCCC
TGCCTACAGAGAGCGCCTGCTAAAGCCCTTTGGCCCTACAGAGAGCCTTCGGCCTGCGGCCATTA
ATATTTTTGTGGAGGAGTATTAGTGAGGGCCGCAGGCGCTACTGTATACAGTCCACTCGCTGCAA
TTGTTCAGCCTTCGTCGCCGGCCAAATATATTTGTCTTTATAAAT
Right flanking sequence: Indices 2168 -- 2667
ATATATGATTGGCAGTTATTTTGGCTATTCCGGGTAGTAATTCTTCCCCGTTTACACAGAAACAA
GAAATAAAGAAACAAGAAATAGATTTATTTTATTAGGCTTGGCAAATTGTAATTAATTGATAAAT
TGATTACATCAAATTTTTCATAACCTAAAAAAACTAATTAGGTTATGATTAGTTTTTTTATACTT
TGGTGAAGCTGACGCCCTTTGCCATGACCTTTCGGGGGCGAGGCGGGGCTCCGCCCCCCAATGGA
CTAGGTCCTTAGAGGGCAGAGCGGGTAAGTGCTTAAGTGGCACCATCTGCTAAGACGTCTAAATG
CTTTCCTTTATAGCCGGAAGTTCTGAGAAGGTATGAAATGCTGGAGGGCTTTTGACCATCCATTC
AAGTGTCGTTGAATTCTGTTCAACAGCCCAAGGACTTGGAGCACACTTGTTTTCACTGGTTAACG
TAAAAAAAACCACTACAAAGAAACAAAAAATTCCTATTACAGAAA
Found at i:2245 original size:15 final size:15
Alignment explanation
Indices: 2225--2253 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2215 CCGTTTACAC
2225 AGAAACAAGAAATAA
1 AGAAACAAGAAATAA
2240 AGAAACAAGAAATA
1 AGAAACAAGAAATA
2254 GATTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.14, T:0.07
Consensus pattern (15 bp):
AGAAACAAGAAATAA
Left flanking sequence: Indices 1725 -- 2224
GAAAATATTCCTTTACTTCGGTTCATCAGGAGTCCACGTTAATCCCCAGTCCGAAAGCGGATTCC
CATTATTTTAAAGTTCCGACAGGAATTGCTCTACGCCACCGTCTTAATTAATTTTAATTAATAGG
CGGCCTTCTTACTTTTATTGATTATCGCCAAGCTGCGCCCGACCGTCCGTATAGGACACGGCCAA
AGCCCAACAAAGAGAGAGAGCTAAAGCCCTGCCTACAGAGAGCGCCTGCTAAAGCCCTTTGGCCC
TACAGAGAGCCTTCGGCCTGCGGCCATTAATATTTTTGTGGAGGAGTATTAGTGAGGGCCGCAGG
CGCTACTGTATACAGTCCACTCGCTGCAATTGTTCAGCCTTCGTCGCCGGCCAAATATATTTGTC
TTTATAAATATATTTGTTTTTATTTGATGATATTTGTTTCTATTTGATGATATATATATGATTGG
CAGTTATTTTGGCTATTCCGGGTAGTAATTCTTCCCCGTTTACAC
Right flanking sequence: Indices 2254 -- 2753
GATTTATTTTATTAGGCTTGGCAAATTGTAATTAATTGATAAATTGATTACATCAAATTTTTCAT
AACCTAAAAAAACTAATTAGGTTATGATTAGTTTTTTTATACTTTGGTGAAGCTGACGCCCTTTG
CCATGACCTTTCGGGGGCGAGGCGGGGCTCCGCCCCCCAATGGACTAGGTCCTTAGAGGGCAGAG
CGGGTAAGTGCTTAAGTGGCACCATCTGCTAAGACGTCTAAATGCTTTCCTTTATAGCCGGAAGT
TCTGAGAAGGTATGAAATGCTGGAGGGCTTTTGACCATCCATTCAAGTGTCGTTGAATTCTGTTC
AACAGCCCAAGGACTTGGAGCACACTTGTTTTCACTGGTTAACGTAAAAAAAACCACTACAAAGA
AACAAAAAATTCCTATTACAGAAACATACGAGCCGAAACTACTAAAGGCATTCCATCCAGCGTAA
GCATCTGGATAATCTGGAATGCGACGTGGCATACCTGCAAGACCT
Found at i:21164 original size:19 final size:20
Alignment explanation
Indices: 21122--21164 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
21112 GGATGTTGGT
* *
21122 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
21142 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
21161 CATG
1 CATG
21165 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 20622 -- 21121
TGGGAGACTTGTCATATTTAGAATCTTTTTGTGGTGTGCTTTGTTTTTTATTATTTTGTACATTC
TCCTTATCATTCAAATATAGGCGCGATACATTGGCGAACAAAGGGCGTAGGCCTAGAATGAAAAA
GATAAAAGCGCGTAAGCGGGCACAGAGAAGAAAGCGCTTGGCGCTTTCTTGGCCTAACGAAAAGG
AGAAACGAAAAAATGAAAAGAGAGAAAAGTTTTACTTTTTATTTTTCTCAAATAAATCAAAAATA
TTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCCTCAACGAAAAAGCCAAAATTTTGGC
TTTTTATTCTCTGCTTGCTCTTTCGCAAGCTGATTATTCTGTCCCTGAAGAAAATAAAGCGCTGG
GCGCTTTCTTGGTTACACCCTACGGGTGTAACCAAGAAAGCGCCCAGCGCTTTGATTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 21165 -- 21664
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCGGCTTATGTGCGACCA
TCATCGTTTTTAAGCCCACGCCATGTAGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGC
CGCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCCAAATTCGTGCGA
AAGGTTCAAGGACTTAGGATGAACTAATGTGAATGGGTATAAGCTTCGTTGCTCAAAAACACCTA
GTACTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAG
TGGCGTTAAGCATTCCCAGCGATACGGAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
CTCCTCGTGGAGTAAATCTCACATCCAACAATCTAACCAGGGAACGGGATAATTCTCACTAAGTT
CCACTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:47539 original size:81 final size:81
Alignment explanation
Indices: 47404--47553 Score: 266
Period size: 81 Copynumber: 1.9 Consensus size: 81
47394 AAGATACTCG
*
47404 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGTCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTTTACCATTTTCAC
47469 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
*
47485 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTTTACCATTTTCA
47549 CCAAG
65 CCAAG
47554 TGAGCTTAGG
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
81 64 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 46904 -- 47403
TTTAGAAACAACATCAGTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATACTTCTCTAT
GTTCTTGTTTGGACCAGCTAATACGAGCAGAGTGATCCATCAGCCATTTTTGCTGATGATATCCA
AGCGTGGGCGCAATGTCTAACGCCCCATCCTTTTATGCTCAATCCACTATACGAGAAGAAAGGGA
AGGATCCAATGGGGTGACGTCACCACCAGAGGCTAACTACCCAGTAACGCCCCACTTTGCCAATC
AAGGCCGCAGGCTTGATTGACAGAGCTGGGGCACGTAGTTTATAGCAAAACTTTTTTTTTTAAAT
ATTTTTTGCTGCGAAAAGCAGCGCCCTCAAAGATTGTAAAGATTTAAGCTAATGGATGATCTGTT
TTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTCTTTTCAATTCAGACATTAAGATACTCG
Right flanking sequence: Indices 47554 -- 48053
TGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTCTGTGTCGTTTTCTTTTCACCAT
TTCATTTTATAGACACCCCCGGCTTATTCCGGCTCGGCCGGACCTGCGGCATTTTTTCAAATATT
TGAAAAAATCTATATTTTGCTGCGCCCTCTGCCTTGAAGTGTGTAGAGACCCCTTCTTTATTGAT
TTATACTAGTCTATCTTAAATCTGAGATAGTGCCGAAAAAATGACTCAATTTAATCTAACCATAG
TCACAAAAACCTTGGCAATGGCAATGACTTTTGTATGACAGGCAGAATACTCCAATAAAAAAGTA
AGCCTCTATTGACTTTATTTAGAACTAAAAGAAGAGAATGCTTCTTTTCGTTGAAGGCTAGAGAA
AAGCAATAAAGTGCAAAGGTTGGAATAAAAAATTTTTGAGCTTTGTTCTACGTAGTTTTGCCATC
TATATAATATAATATAGTAAGAGATAATAAGTTGGCGAAGAAGTA
Found at i:95121 original size:15 final size:15
Alignment explanation
Indices: 95101--95130 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
95091 TAGGGTACAA
95101 TCTGAATTCTAAGAT
1 TCTGAATTCTAAGAT
95116 TCTGAATTCTAAGAT
1 TCTGAATTCTAAGAT
95131 GGTCATAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TCTGAATTCTAAGAT
Left flanking sequence: Indices 94601 -- 95100
AAAAGATAAATTTAGGTAATATGCAATAAAATAAAGCATCAAGCAATTGGTAAAAAGCGAACACC
CTGTAAAAATAAACTAATCATGATGTGCTCTTTTCCAGTTGATTATTCGGCACATTAGGGTAATT
AGCTCAGTTGGTAGAGCGCCTCGTTTACACCGAGAAAGTCAGCGGTTCAAGTCCGTTATTACCTA
AGGGTTTCCATTATCTGTAATTATGAATTGAATCTAGCGTATGGATAAATTTACTAATTTTATTA
ATGGTGGTAGAACCGCAATAATTAAAAAAAGGGGGCTTTTAGACAAAAAGCAAGCCCGCTTGATT
CGCATGGCAAATGAGAGCTAATTATTCTGAAAAAGAATAACACAGTTAAAGGAAACATAAGAAAG
TGGCGAACGCAAAGCAAAAAAAGCGATAATATATATTATCGCTTTTTTTGCTTCGCGTTTGGGCC
AACTAAAGCAGAAAACGCATGGCGTTTTCGTAGTTTAGGGTACAA
Right flanking sequence: Indices 95131 -- 95630
GGTCATAAGACAAAAAATATATATATTTTTGGACGTTTTTCTAATTGAAAAGTGCCCCGGTTCCA
TGCAAAAAGCAGGGCTCCACTGGCATAGCGTAGAGGCCGAAGGGCTTCGCCTAAAAACCGATCTA
GACTTGTTGCATGCTTTGGGGCCATTACGCAGTAATGGCCCAAAGCATGCAAAGCCACAGGTCAA
CTAACCTTCCTCCTGCCAAGTGCCTTCCAGTGCGAAGCAAAGAGCCGCGCGCCCTGACTGCGCGC
GGCTGCTGGCGATATTAGCCTCGTGGCTTCAGGTTACTCTCTTTTCCCTGAAAGCTTGAACGAGG
CTTTCGGAGAAAATAGAGTTTTCACTTTCGGATTTCTACTGACGTAGCCAGTAGAATGGAAAAAT
CCCGATGAATCATCGTAGATGATTCATTATGTTTGGGAAAATAGCTTAGTTGGTTAGAGTGCTGG
TCTGTCACGCCAGAAGTCGCGGGTTCAAATCCCGTTTTTCCCGGT
Done.