Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_049004
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: 228021
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:41191 original size:17 final size:19
Alignment explanation
Indices: 41155--41191 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41145 CTGATCTATC
*
41155 TAGGATGATCTGTTTTCTT
1 TAGGATGATCTGTATTCTT
41174 TAGGATGAT-T-TATTCTT
1 TAGGATGATCTGTATTCTT
41191 T
1 T
41192 TTTATGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (19 bp):
TAGGATGATCTGTATTCTT
Left flanking sequence: Indices 40655 -- 41154
TGACTATATTCATAGTGAGGAGCGTGATTCTACGTCTGACTCCTTCAGAAGTATATCTAATTTTT
TCACCTTTCAATTTGAAATCACACCATCGTTCCGTATCTATTTCTTCCCCAACCTCTACTCATTA
CCAAAAGAAAAGTGGGTCACACATACTTTTGAAGATAGCTTGAAGATATGAGTGTTCCCCTTTTC
CCCTGAGCTCATTGTGCCTCTACTTATGTAAATGAGAGTCCATCTTGCTTACTATGTTCGTGACA
GCTACCGAGACTCAAGCTTTTCTAGAAAGCTTCTCAGAGATCCAAATACGTTCATTGTGACTTGG
AAGAAGTAATAACGTACTAATACTCGGCGGAAATAGAATTTTCACTTACAACATCCGGATTATGA
ACTTGACGAGTTACCAATTACTCCGCGAGCATCATAATCATAAAGGCTTTGGAGGCCGAAGAAGT
ATGTTTCTTCTGGTCTGCTTATCGCCTGCTATGTCCTGATCTATC
Right flanking sequence: Indices 41192 -- 41691
TTTATGATCTTGGCCTACTTACTGCTTAATTCTCAACGCCACCATAAGAGGAACTTCATTTCATG
GAAGAACTTCGCTTCCTGTGTGCAAGCCAATTTCTTCGGTTTAACATGCGGCGTGTTCGTTACAC
TTCCCATATCACTATGACTAGGGCCATTGCGACCAAGGCGGCGGGATGTTGAAGGCTAGAAGCCG
AAGCTAGAAAGAGGCTGGTGAGGGCTGGAGGCATCTGCCATTCACTCCTCCTTCAGGCTTCTAGC
TTGAGGCTAAAGGTTAAACAAATTTGTACCGAGCTTAAGTTAACAGAAGGCAAGACTGTCCGCGA
GCCAGACGGCTAGAAAAAAGGTAACAACCTTCCGAGAAAACTAGCCTATCGCTTGGCTCTGGCAG
AAAAAGGCACGCAACACATGTTTTGAAAAGGCTTTTTTGTGCCTTCGGCCGCCCCTTCGCCCCTT
GCGCGCAAAAACCTAGGAAAAAAATTTTTACCTCTTTTTCTCGTA
Found at i:67209 original size:19 final size:19
Alignment explanation
Indices: 67182--67219 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
67172 TTCTAATTTT
* *
67182 GGATTTAGTTCTAGATGAA
1 GGATCTAGTTCCAGATGAA
67201 GGATCTAGTTCCAGATGAA
1 GGATCTAGTTCCAGATGAA
67220 AATCTAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
GGATCTAGTTCCAGATGAA
Left flanking sequence: Indices 66682 -- 67181
GAATTTTGACTCTTCACCCTACTGTTCGACTCTCTCTATTATTTATTTGGAATAGGTTATTTTCT
CCATAATCACTAATGATGACAGCAGTCTTCTCACGCTAGAATGCTTGCCATAAACTCAGATTAAA
AGGCTTATTTCCAGACACTAAAGAGAGCACATACCAACCTTCAAGAAACAGCAGCACAGGACGCT
CAGGCTAATGACAAGTATACCAAAAACCAAAAGGAGACCTTATCTTTCATTTGTTTGGGAAAAGG
TACCAAAAACACAAAACATTAGTTCTGTTTAGTACACCAAGCACGCGGTTCTGTGTAAACTGTCA
TATTTCATGACAGAAGTTCGCTTCTGTCTCAAGCTGACCATTCAGGCTTCAAGTTAAAGTCTCAG
ATAATCCGAAGGCATTCGTGAGAATGCCGAGGCGAGCCTACGGCAACCGAAGACATGCGATAGCT
TGTTAAGGCGGCGCGCAAGGCAGGCTTTCATCTAGTTCTAATTTT
Right flanking sequence: Indices 67220 -- 67719
AATCTAATCTTAAGATCAAAATAAAAATGAAGATTTAGTTTAAAATATCAAGACTAAGTATCAGG
CAAGCTTCGCGTTCTGTTACGAGGCCGAAAGGCTAATCTCAGGCAGGGCGGCGGTTATCAAGCAA
GCTAAGCTTGGTTCATAGTTTTGGAGCAAACATGCAGTATTAAGCACGCGCAGCTTAGATAGGGT
CGCATCACTTATCCAGGAAAGACATCCGCCTTTAGCTAAATGTCGCGCTTTAGTCATGAGCGAAG
CTACTCTGACTTTTGGCTGCAGCTAGCTTCAACAACGAAACATCATATGAACCATCATATGAATC
ATCGTATAAATATCATATATAAGGCGGCTTTCTAAGAATTGCCATAAACCATAGGGCACTACTTG
AAGTCTTGATTGTCTCAGCTTTGATGTCAAATGTAGCGTCTGGATTTACTTTGCAAGTGGCTAAC
TCGGACTTAGGATGGTGTTCTCTCGGTCTATATGGAAACAAAAAT
Found at i:119589 original size:20 final size:20
Alignment explanation
Indices: 119564--119604 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
119554 AGCGTTATAT
119564 CTAGATAGAAAAGACTAATG
1 CTAGATAGAAAAGACTAATG
* **
119584 CTAGATGGAAGGGACTAATG
1 CTAGATAGAAAAGACTAATG
119604 C
1 C
119605 CTGCCGAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (20 bp):
CTAGATAGAAAAGACTAATG
Left flanking sequence: Indices 119064 -- 119563
GGCTTCTGCATCTTCCTTTCCAGCTCTTGTGAATATGCACGACGAGTTTCCATCCAAAATGATGA
ATCACAGCCTATTTTGTTAGTAACTGGCTTTGAGGATTTACTTGCAGAAATGGCTAGAGATGCCT
GCCTCTTATGGAGCCCAAAGTAGACATCGAATGGAATCTTCAGATGGTCTCATGGTTGAGCTGAG
GAAGGGAATGTGGCATGATCCAAAAGTGGCCTCTCCTCTACCAGAAAATCCAAAATATCCTTATT
TTTTCGACACAAAAACAACCAAGAATGGACTTCTATGGAGGGGGGATCGGATCAGCGCAGATCCA
TGTATGCAGGTATTCTAAGCAGAGGGGAAATTGTTCCGATTCTGTTGGAAACGATTATTAGTACT
GCTATTTTGACTAAAGGCCTTACACCTGCGCCAAAAATCCCCCAGGTGCTGACGGTACTTCAAGC
GGTGGCTCGGGAAACGTTTCTGATCTTATGAGAGAAGCGTTATAT
Right flanking sequence: Indices 119605 -- 120104
CTGCCGAGAATCTCCAAATAAAGGAAAAAAATTCTATAGAATTTTTTCTTGCAGATTACAGTTCA
TTCATTATTTCCTCTGGTTCGATGAGCAGAAAGTCCCAAGAACAGCAATCCTTCTACAAGCCAAA
AAAGCGCGCTTTGCGCTCAGAGAACTACCAAATAGATCCGTTTTTAGGTTGATTAGACTTATCTA
GACTTTCGGACTTAACTGGTTTCGTATGGCCAAGCATGCCATTACATAGTAATGGCATAAGAACC
CGATGCCATTACTACGAGCTTTTATCTAGGAAATAAGTACGTGATGAGCCCTGGGGTCACCGCCG
CCGCGAGCATTTGCCCGCTGCATCATACCTTAAAAGTAAATCAGGTTAGCTGTAGCCTTCGTCTT
TAGCCTTAGCCTCCTTCTCCCTTTCTTACTCTTTCTCTGTCATCCTTCTCCTCTTGTTTGACAAG
CTACGATGGCGTAAAGAAACCTAAGCGTAAAAGCGATCTAAATCT
Found at i:196251 original size:32 final size:32
Alignment explanation
Indices: 196206--196272 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
196196 GATGCGCAAC
*
196206 AAACGCATGTAGCGTTCTCTAAC-GAGAAAAGA
1 AAACGCATATAGCGTTCTCTAACAG-GAAAAGA
196238 AAACGCATATAGCGTTCTCTAACAGGAAAAGA
1 AAACGCATATAGCGTTCTCTAACAGGAAAAGA
196270 AAA
1 AAA
196273 AAGAGGAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (32 bp):
AAACGCATATAGCGTTCTCTAACAGGAAAAGA
Left flanking sequence: Indices 195706 -- 196205
AGGAGCCATATAGACTTGTCGGGTTCCACCCTACTTAAAGTTCAAGTTAAAGGTCGGATGCCTCC
ATGGCGCCTCTCAAAACCTCTAACTTAGATAGGATGGTGCCGTCAATGGCCTCCCAGTTTAGGCG
GGGTGCGATCCTGTATTTCGGCTGAGGTAGGCAGTGATCATAATTCTATGTTACGCCTTCTTTTG
CTGGTAAGATGGTGGTTTCACTGCCGTTACGAAAGCTGGAAATCCAAAAAAAAGTCCACACAAAC
ATCAATCCCATCTTGCATGGTGGCAGGCACTTCTCTTAGGAAGAGGGATGGACTCCGTGGATGGT
GTAGAGTAAAATCCGCAAACAAACATGCAGATACATAGGCCCCTTTCCCTCCGCTTAGTTGTTCT
GCACTTTCCGTCTGCACGGCCCCCGCTTTTGACAGGGTTAGGATTGTACTATGGGCCTTCTGACT
TCAAGCTATGCGCTGCGCGCTGCGAAGCGAATAAGGATGCGCAAC
Right flanking sequence: Indices 196273 -- 196772
AAGAGGAGAGAAGATAACACGGTTTTTCTCTCTTTGCGTTTTCTCGAAGAAAAACTTGTTCTCCT
CTCCGAGCGCGGCGAATGAAGGCGCGCTGCGCTTTCGAAAGCGCGGATATTTCTTTTATCTCCTT
GTTTTTGCTCGCCAGGCCGTAGGAGAAACCGCTTCGCGCTTTATCAAAAAAGCATAGCAAAAAAA
GAAATCTATCTTTCTATTTTTTACAGCGGCGCGTTTCCTTGGGTTGCCGCTTAGCTGAATCTCGC
CGGTGTCACCTATAGGCTGTGACGTTTGGAGTTGTCGTTTGTGCACTTGTCCCCAATGAAATGAG
TAATCCACTCCCCTGCCAATTATGGCCTTACCACTTAGTCTCGATGGCAGGCGGGGAGTATAGCA
GCTTACGTTTTCCTCACGTATGCTGGACACGTGTCAGCTGTAGGAAGTATTGTTCCGAAAGTGAC
TTCGATTTGCCAATTCAGGCTCAACTCGCTGGACGTTAGCGGACT
Found at i:202166 original size:13 final size:13
Alignment explanation
Indices: 202148--202172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202138 TCCTCCCATT
202148 CCTTCTTTCTTGG
1 CCTTCTTTCTTGG
202161 CCTTCTTTCTTG
1 CCTTCTTTCTTG
202173 ACTCCGCTTC
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:0.00, C:0.32, G:0.12, T:0.56
Consensus pattern (13 bp):
CCTTCTTTCTTGG
Left flanking sequence: Indices 201648 -- 202147
GAAAAGGGAAGAAAACTTTTCTTCTCCGAGCGCTCTCCAGAACTCGAATTTTCGAAGACCGAAGC
TACGGTGGTATCCGAAGGGTTAAGTGCCTTTTCCGGTTATCTCCTAAAACTACGTTCGTGTCCGA
AGGTTGAGGTGCTGGTGTTAATATTTTCTTCCCAACATCCCTAGCATGCTTTTGAGCCTCGGCTT
CAGATACTTTTCAGAAAGAACAGGAAAGAGAAAGAAACGAAAGAGGGAGGAATGCGCCAGAATCT
CTCCAACCGAGTTACTTTCCTATAGAACCTACAAGAGCGTACTGGCCTCCCCTACAGCTGCTTCA
GACTTAGTTAGAGCTTTATTTTGCCTCTTTGTAAGCGAGAACTTGCGACTAGTCAAGCCTAAGCT
AATCACGACAATCTATCGCGTACTCTAAATCCTGATTTGCATCCCTCATTCTCTACCCTGCCAGC
TGATCATGAGGTTTTCTGCCTGCTTTACTTCGACCTCCTCCCATT
Right flanking sequence: Indices 202173 -- 202672
ACTCCGCTTCGGAATGCCCATTGGAGTTCCATACCGCATAACCACCTTCTGCTGCGGCCTCGGAT
AGCAGAATAGAAGTTCCCTCCAAAACTTCTAGAGTATTTTCCTTCGCTGGGTCGGCGGCTGTCCC
CGTTTGTCCAGCACCCTTCTGCGCCGCCGTGGCCTGCACTGCCTCCGAAGATTTTTTCCTTATTC
TAGCCATGTGGAGCAAGTTGAAGAAGTGGCAGCTAGACAAACGAAACTGACCAAAGAGTACATGA
ACTGCAGATATATATAAGGTACAGGCGTTCATCTAAGCGCTACTTTTAGCTAGCGCATGTAGATG
GCAGTCTAAACCCGTCATAAGAATCTCCTAGGTGAATGCTAAGCCCTCGCCCTCCAGGGTCTCAT
CGTAATTCCTTCCCTCTGTTTCCTTTTCAGTTTCCTAGGGAGATGCGTCTTCTTCTCTTCAATCA
ATCAAGGCAAAAGACAACAAGCACTAAAGATAAGAATCAGCATGA
Found at i:214405 original size:81 final size:81
Alignment explanation
Indices: 214270--214419 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
214260 CTCAAGCTCA
*
214270 CTTGGTGAAAATGGTAAACACGACAGACTTAAAATCTGTTCCTATGGGTTATCGGTTC-AAGTCC
1 CTTGGTGAAAATGGTAAACACGACAGACTCAAAATCTGTTCCTATGGGTTATCGGTTCGAA-TCC
214334 GATAGTGAGCATACTCG
65 GATAGTGAGCATACTCG
* *
214351 CTTGGTGAAAATGGTAAACACGACAGCCTCAAAATCTGTTCCTCTGGGTTATCGGTTCGAATCCG
1 CTTGGTGAAAATGGTAAACACGACAGACTCAAAATCTGTTCCTATGGGTTATCGGTTCGAATCCG
214416 ATAG
66 ATAG
214420 CGAGTATCTC
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:0.20, G:0.23, T:0.28
Consensus pattern (81 bp):
CTTGGTGAAAATGGTAAACACGACAGACTCAAAATCTGTTCCTATGGGTTATCGGTTCGAATCCG
ATAGTGAGCATACTCG
Left flanking sequence: Indices 213770 -- 214269
GCTTTGCTCTTTGGTTTGTTTTGCAAACGAAAGGAAGAAATAAAAGAAGCGGCGCTTTTTTTCCT
TAAACCTTTAGGATGTCTTAGTCTTTCTTTAGCCAAGAGAGTCTTCCGCGAGACTCCCAGAGCTG
ATTTCTTCGAATCTTTCTTTTCTTGAAAGCCGTGTCATACAAAAGGCATGGCCAAGTGCACTCTT
GCTGGCAACTCGTATCTGAAGACTGGTACAAAGCCGTAGAGAAGAGGTTTTACAGGCTTTGAATA
CAGAAGAGCGCTCTACTATCGACGCAGCCCACAGAGGGTGGGCAAAGTAGGGCGGCGGCATAATC
GCCCCACACTTTCCTACCAAGAAAGGCAAAAGATCTAGGGGTCGCAGATCTGGTCAAGCCAAAGG
AAGTCTCGTATGCCGAAGCCGAGGTGGAGATGTCTAAAGAAGAAAATGACGAAGAGAAAGCAAAA
CAGAAAGATTTTGTCTCCGTTCTGCGCTTTGCTTTCTCAAGCTCA
Right flanking sequence: Indices 214420 -- 214919
CGAGTATCTCAGTGTTGAATTTGGAAAGAAAGGCGGATATAACTTAATGGGTTGAAAGTGTCAGA
TTGTGAATTTGAAAAAACGGGTTCGAATTCCGTTATTCGCCAAAAACAGATCATGAATTAGCTTG
AATCTTTACAACCTTTGGGGCGCTCAGAGAAGAAAACTTGTTTTCTTCTCTTGCCAAAAATTCAG
AGAAGAATAACCAAAAAAATTTAAATTTCTTAGAAAAGAAAAAAATCTATTTTTTTTTTGCTCGC
TAACGAAGTGCCGCGCACCTGACCAGCGAGCGGGTTCGCTGCTTAGTGGAAAAAAGAGAACGCAT
TTCTTTATCTGAGCTTTGCCATGAACTACATGCCCCCTTGGCCGCCGCCCATCAAGTGTTTTGCA
CCTTGATGGGCGGCGGCCAAGTGGCCTCCTCCCCTGCGATGGATCCTCTGGTGACTAAGTTACCC
CTTCTGTATCCTTCTGTCTTTCTGGAGATAGGTAGGCTCCAAGCT
Found at i:214959 original size:13 final size:15
Alignment explanation
Indices: 214918--214952 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
214908 AGGCTCCAAG
*
214918 CTTCCTTCCTCTT-T
1 CTTCCCTCCTCTTCT
214932 CTTCCCTCCTCTTCT
1 CTTCCCTCCTCTTCT
214947 CTTCCC
1 CTTCCC
214953 CTCTTCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (15 bp):
CTTCCCTCCTCTTCT
Left flanking sequence: Indices 214418 -- 214917
AGCGAGTATCTCAGTGTTGAATTTGGAAAGAAAGGCGGATATAACTTAATGGGTTGAAAGTGTCA
GATTGTGAATTTGAAAAAACGGGTTCGAATTCCGTTATTCGCCAAAAACAGATCATGAATTAGCT
TGAATCTTTACAACCTTTGGGGCGCTCAGAGAAGAAAACTTGTTTTCTTCTCTTGCCAAAAATTC
AGAGAAGAATAACCAAAAAAATTTAAATTTCTTAGAAAAGAAAAAAATCTATTTTTTTTTTGCTC
GCTAACGAAGTGCCGCGCACCTGACCAGCGAGCGGGTTCGCTGCTTAGTGGAAAAAAGAGAACGC
ATTTCTTTATCTGAGCTTTGCCATGAACTACATGCCCCCTTGGCCGCCGCCCATCAAGTGTTTTG
CACCTTGATGGGCGGCGGCCAAGTGGCCTCCTCCCCTGCGATGGATCCTCTGGTGACTAAGTTAC
CCCTTCTGTATCCTTCTGTCTTTCTGGAGATAGGTAGGCTCCAAG
Right flanking sequence: Indices 214953 -- 215452
CTCTTCTTAAAAACGCACGTTATAGTTTCCCATCATACGCCTCTAGTGTCGAAGAAGATTTTAGA
CCCAGGCTACCAGGGTTGCCCCTGACTTTTGGCTCCAGCAATTATGCTATTACTAAAATGTTCTG
CTACTTTGCAAGTTGTGTATATGGCAACGTTGCGATTGACCAATACGCGCGCAGCAAAAGTCTTC
ACCTGAAGACGTGGTCAATATGAGTGGCTTTTTAAGTCTTTTGTCACCCCCCGAGTCAGCACTTT
CTCTTTCTGGAGGCGAATGGTGGCCTATCTCACCCTTTAGGGTGAGCTTTCGCTCTTTGGATTGT
TTTCTGTCCTGGTATCTGATCCGATGACTAAATATCCGTTTCAGGAGCCCCTAGATTTTACCCCG
TTAACAGCTTGACTCTAGGGCAAGATTTGGCGATCTTGTATACTCCGGTTATCTTGGACCGATCA
GGGCATGCAAAAGTCTATCGTGCCCTCCGCGCCTACTCAAGGACA
Done.