Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_021399
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: 450826
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:114527 original size:21 final size:21
Alignment explanation
Indices: 114503--114545 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
114493 TCAAGGGGGG
*
114503 GTGCCATCTATACAAGAAGAA
1 GTGCCATCTACACAAGAAGAA
*
114524 GTGCCATCTACACGAGAAGAA
1 GTGCCATCTACACAAGAAGAA
114545 G
1 G
114546 AGGAAGCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (21 bp):
GTGCCATCTACACAAGAAGAA
Left flanking sequence: Indices 114003 -- 114502
ATGGTTGGCTAGCTTCAAACAAAAGAAAAGGAAGAAGCCCTAATCTTCGAGTCAGGAGGTTAGAT
ACCCACCATATGAAGTAGCTTGGCTTGTTAGCAACCTTTGGATAACTTGTTAGTCCTTTGATTGA
GACCGAGCCCTCACTTGCCGAGCGAACCTCTTCTTATTCTCCTTCGTTCGCAATCCCACCTTGAA
TTCAAACCGACGATTCGACAACAAAAGGAGTTGTCGTCTGGCATCACTACTTGAAAAGCTCGTAC
CAAGTCAGTGTTCGTTGCCATACTCTGAGGCTAGTGTATCTGACACAGTAGAACTCCCTAAACAA
TAAAGAACGGGACCCTACTAATAGGGTAGGGAAAGATCCCACTGTTTCTGGACCAACCAAACCAC
TGTATGCGTATCAGGAAATGCTGCTTCGGCTGCTTTTGCGGAGGCAAGGGAAGATAGATTCATCA
GGGTAGTCTCGTCTATACGATTCTGCCGGGTGGACTCAAGGGGGG
Right flanking sequence: Indices 114546 -- 115045
AGGAAGCGAAGTCAGATGCTTCATATGCCTCTTCTCGCTTAATCATCCCCTGGATTTTGAAAATG
GCCTTCCAAGCCCCAACCTATCATCTCGGAATCGAATTCATTTGCTTTTGCAGCGTCTGCATATC
GATCGGTTTCAAAACCCTCGGTATCGGCTTCAGCCTTCCCGGATCCAACCTTCTCTGAACTCTTC
TGACCCCGCCGGCCCTCTCGCCTGAGCCCTTTCTTTTCAATAGGATCAAGGTGCTCTAAGATTTC
AGTTTGCATGCACTAGTATAGTAATCGATTGCTCTTTAGGAAAAAGATGAGAACAAGGCGGTCTC
ATAGGTTTCCTTATCAGCCTTCTTATGGGAGGCATGCCAACAATCTTTCGTGAAGACCGCATATT
TGTCGGTGCGAGTTTAGCGAAGCTGGGCTCATTTATGATCCGCTGATCACAGAGCATTAGGGGAA
GGATTTCTCTCCAACAAAGTAGAAGTAGGCTTTGCTTGCTCGCTA
Found at i:136267 original size:42 final size:42
Alignment explanation
Indices: 136208--136292 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
136198 CGAATTCGAC
136208 TGAGACATCTTCCATTCCTAATAGTCAGTCCACGACTACTAT
1 TGAGACATCTTCCATTCCTAATAGTCAGTCCACGACTACTAT
136250 TGAGACATCTTCCATTCCTAATAGTCAGTCCACGACTACTAT
1 TGAGACATCTTCCATTCCTAATAGTCAGTCCACGACTACTAT
136292 T
1 T
136293 AGTAGTTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (42 bp):
TGAGACATCTTCCATTCCTAATAGTCAGTCCACGACTACTAT
Left flanking sequence: Indices 135708 -- 136207
TCTTTCCACACCTCCGGATATCTGGTGCCAAATCGTCGCCTCTTTCCTGATTTCTTCGATAATCG
AGTTGGCGGTATATGTGGCATCGATTGTACAAGTTCGTGAAGAGGGCTGGACGAGTAGAATGAGG
GAGAGCGGCTCGATCGACAAAAAAGAGGAGTAGCCCCCCTGGAAAAGTCCCCCTCAATGAATTCC
CGAGCCATTCTCAACCAACATATGCGATTCATTCCCGTACTGCTCCTCAAACACAGAGGAGAAAG
ACCCTGGGAACCGGGGCCTGGCCCATCCCGACAGTTCATGCCGGGCGGCGTGCGATCTACCGGTG
GAATCTGACTGGGGGGGGTCAGATCAAGGGGGGGTTCAACGAAGTGAAGAGAAAGGAAAGAAAGA
ATCCATTTTTTCACAACCCGGTTGGAGGGTAGGCTCCGAAATGGTTAGGAAATAGCAATAATGAG
ACGGATATTTTTATTTGATGAACCCTCTCTGAATTCGAATTCGAC
Right flanking sequence: Indices 136293 -- 136792
AGTAGTTATGGTGGGTTTGAATCGTCTAATACTCAGGCTTCTTCTCCTTCCTCTGGTATTTTTGA
GGATCATCCAGGTCTGAACCCGTCAAGTGAGCGCGTAGTGGAGCTGGACTCTGCTATACACGACA
AAGTCGGGCAACTTTGTCCTAACAAAAGTCCTGAAGATATTACGGCGATGGCCGAAGCCATACAT
GGCGAAAGCAATGACGTCGCTTTTCTTGAGCACACCCTGGCCGATCTGAACCAAAACGGAGTCTC
AGGGGAAGCCTTTCAGTGTGCCATAGATTTTTTTGGGGGGGGAGCCCCCAACCCACTTGACCAAT
TTGCCATTAACCCATTGATTCTGATGAAGGTGGGAAAGATCTATTTCTCATTCACAAATCCATCC
TTGTCTATGCTGCTCACTCTCAGTTTGGTCTTACTGATGCTTTATTTTGTTACGAAAAAGGGAGG
GGGAAAGTCAGTGCCAAATGCTTGGCAATCCTTGGTAGAGCTTAT
Found at i:136295 original size:21 final size:21
Alignment explanation
Indices: 136229--136295 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
136219 CCATTCCTAA
136229 TAGTCAGTCCACGACTACTAT
1 TAGTCAGTCCACGACTACTAT
* ** * * * *
136250 TGAGACA-TCTTCCATTCCTAA
1 T-AGTCAGTCCACGACTACTAT
136271 TAGTCAGTCCACGACTACTAT
1 TAGTCAGTCCACGACTACTAT
136292 TAGT
1 TAGT
136296 AGTTATGGTG
Statistics
Matches: 30, Mismatches: 14, Indels: 4
0.62 0.29 0.08
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (21 bp):
TAGTCAGTCCACGACTACTAT
Left flanking sequence: Indices 135729 -- 136228
CTGGTGCCAAATCGTCGCCTCTTTCCTGATTTCTTCGATAATCGAGTTGGCGGTATATGTGGCAT
CGATTGTACAAGTTCGTGAAGAGGGCTGGACGAGTAGAATGAGGGAGAGCGGCTCGATCGACAAA
AAAGAGGAGTAGCCCCCCTGGAAAAGTCCCCCTCAATGAATTCCCGAGCCATTCTCAACCAACAT
ATGCGATTCATTCCCGTACTGCTCCTCAAACACAGAGGAGAAAGACCCTGGGAACCGGGGCCTGG
CCCATCCCGACAGTTCATGCCGGGCGGCGTGCGATCTACCGGTGGAATCTGACTGGGGGGGGTCA
GATCAAGGGGGGGTTCAACGAAGTGAAGAGAAAGGAAAGAAAGAATCCATTTTTTCACAACCCGG
TTGGAGGGTAGGCTCCGAAATGGTTAGGAAATAGCAATAATGAGACGGATATTTTTATTTGATGA
ACCCTCTCTGAATTCGAATTCGACTGAGACATCTTCCATTCCTAA
Right flanking sequence: Indices 136296 -- 136795
AGTTATGGTGGGTTTGAATCGTCTAATACTCAGGCTTCTTCTCCTTCCTCTGGTATTTTTGAGGA
TCATCCAGGTCTGAACCCGTCAAGTGAGCGCGTAGTGGAGCTGGACTCTGCTATACACGACAAAG
TCGGGCAACTTTGTCCTAACAAAAGTCCTGAAGATATTACGGCGATGGCCGAAGCCATACATGGC
GAAAGCAATGACGTCGCTTTTCTTGAGCACACCCTGGCCGATCTGAACCAAAACGGAGTCTCAGG
GGAAGCCTTTCAGTGTGCCATAGATTTTTTTGGGGGGGGAGCCCCCAACCCACTTGACCAATTTG
CCATTAACCCATTGATTCTGATGAAGGTGGGAAAGATCTATTTCTCATTCACAAATCCATCCTTG
TCTATGCTGCTCACTCTCAGTTTGGTCTTACTGATGCTTTATTTTGTTACGAAAAAGGGAGGGGG
AAAGTCAGTGCCAAATGCTTGGCAATCCTTGGTAGAGCTTATTCA
Found at i:221412 original size:5 final size:5
Alignment explanation
Indices: 221402--221471 Score: 140
Period size: 5 Copynumber: 14.0 Consensus size: 5
221392 CTGCTTCTTC
221402 TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG
1 TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG
221452 TATAG TATAG TATAG TATAG
1 TATAG TATAG TATAG TATAG
221472 AGTTGAGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 65 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TATAG
Left flanking sequence: Indices 220902 -- 221401
TGTATATGGATAGGCCAATTAACAGGATCATAATAATGCATGCGATAGATGGTCATGGCAAGGGA
TGACAATGTCATCACATCCTCGATATCAACATTGTACTGAGTCCAATAGATCTCTTGAGCCTTCA
CCATCACTCCTCCTAAGAGCCTGATATCTTGCCTCAAATACATCAACAATTCGTCACTCAGATCC
ATCAAATTGGAGACTTTCACATCATCATGATCTATGGAGCCTTTAGACCCTAATTGAGGGCATAA
CGTCTGAGCCAATGATGCCAGACTGCCTGGGAGCAAAGTGCAGGAATCTCGGAAACGGAAGAGAA
ACTTCTTTCCAAGATACACTTTCAACTCGTCAAGCATATGGTTCCTCATCAGTGGCTTGATTGTA
TACTTGTTTCCACGATCCGCATAATACCTGAGTAGGAGAATTCCATCGAATCGCGCGAAATTGTG
GAAGTAAACAGTTCGAACGCCTTTATAGGACTTCACTGCTTCTTC
Right flanking sequence: Indices 221472 -- 221971
AGTTGAGAAACTCGAAGAACATTCTTTGACTCCTATCTTCAAACTCCGCGAGGAAAAGGATGTGA
GCCTCACTGCATGCGTCGACTCCGGTTCAGACCTCAACTCAATTGTCTCCGGCAAGATTCTTTCT
CCAGGATGGGAAAATTGCACCGAAAAGGCATTCGCGGTGAATGGATGACCGCTCCAGATTCCGGA
TATAGTGCAGGCACATGCGCAATCAAAGTCTCTCTCTGCCAACAGCGTCGACTTTGTCCTGCTGA
TTCGAAACCTTGAGAATGAGTGCCTCCTGGGGACTCCCTTCCTATCAGCAATAGACAGAATGGAA
GTAATAAGAGGAGAGAAGGGTGGAATCGACGGCTTCCATGAAAGGACTGCCTGATTCCCATTCCC
GGATCCTCCTCGTGTAGCGAGGATACAGCAGCTGACGCTCAAAGAAGAGGCCATTCATGAGGTGT
TGGCCCGAATGAGGGAAGGGCTCAACTATCCCTAGTCGGACCTTT
Found at i:260314 original size:22 final size:22
Alignment explanation
Indices: 260286--260331 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
260276 GCTGGCTGCG
260286 CGAGTCACCTTCTTCTAAGCTC
1 CGAGTCACCTTCTTCTAAGCTC
260308 CGAGTCACCTTCTTCTAAGCTC
1 CGAGTCACCTTCTTCTAAGCTC
260330 CG
1 CG
260332 CTGGACGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.37, G:0.15, T:0.30
Consensus pattern (22 bp):
CGAGTCACCTTCTTCTAAGCTC
Left flanking sequence: Indices 259786 -- 260285
ATGAGGAGAAAAGACTGCAAAATCTTTCCGAAGTGAGAGAAGGAGGGAAGGCGCTCCCGCGCGCT
ACAACTAACAGCCTGCTGAAAAACGCGACGCTCCGCGCGCAGCCCCCACACCTCCTCTCCCCCGC
TTGCTGCTCACCTCAGACACGGGGTTCCACTGGGGGGTCGGCATTCCTACGTGCTCCTCCTTGCC
CCCTGGGACCCCTTCGGGTCACCTTTGGAAAAGGCTTTGTTCCCGAAGCCGGGGGGTTGTTGGAT
GGATTCCGTGGGGGGATTCTCCCTCCCTCCAACTCAATCAATATCAACAAAAAAAATCCGGCTTG
GTTGAGTCAGAACAGTTTCGGGGGTTCATTGATTAGTCAACGTCACGGTGCTGGTGACGGTCGGG
ACCGTGGTCGTCCGTCTCCGGTTTGCCGGCCGATAAGATCACTGAGATTGACCAGCCAGCTGGGT
TGGTTTGGCTATTCCTTTCTATTCCAAAGGAGTCAGCTGGCTGCG
Right flanking sequence: Indices 260332 -- 260831
CTGGACGACACGGCATTCTCGTTCAAAGAGGGGCCGGCCGTACTTGTGATGGTTCCCCGGGATCC
AATAAACCCACTGAGGTCTACGTTGCCACGATATTGTTCCCTGTCAGCAGGCGGGCTGCTTTTCC
AAAGTTCGGCCCGGTGGGGGGTTGGGGGGCCTTTTGGACGCATATTCTGTCGTACCGGCATGGCC
CCCACTGATTTGTTTTCGATCGGAGCATCAAGCAGCGCAACCCGGTTCTACTTGACTAAGCCCCG
TGCTCGTCCAAGGAGGGAGTTTGCTTTACCCAACTCCCTCCGACCCGACATTCATGAGTTTCGAA
TGAAGAATGAAGAGTGCCCTGCCCCTCTTTTTCTTCCATCGTCGGATTTTGAAGTTGGTAAAGAC
CCACCCCTTGTTTCAGTCAGAATGAGTCCCCGGGACCCCGGGACATTGGCTTCCGCCAACAGTGA
ACTCTCCAGGATCGCATCCCGCGCATATTCTACATTATAGCCTGC
Found at i:284932 original size:24 final size:21
Alignment explanation
Indices: 284882--284933 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
284872 TCTCAGTTTT
284882 AGAAGACAATGAAAGACTAAC
1 AGAAGACAATGAAAGACTAAC
* *
284903 ATAAGACGATGAAAGGAAACTAAC
1 AGAAGACAATGAAA-G--ACTAAC
284927 AGAAGAC
1 AGAAGAC
284934 TCCTCCGCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
24 12 0.48
ACGTcount: A:0.56, C:0.13, G:0.21, T:0.10
Consensus pattern (21 bp):
AGAAGACAATGAAAGACTAAC
Left flanking sequence: Indices 284382 -- 284881
AGTCAAAGCGGTTGCTATTGTTTCAGCTTCTGGAACAGGGAAAGCCCTTTCCTTTTCTTTTGATT
TGGATGCCGGAGCTTCTTCTCGGGATCAAGGATCAAGAGGTCAAAAAATCAGTCAATAAGTGAAA
GACTGACTCTCTTTTACCCGTTTGAGTATACTACTATTGAAAGACGGCATTTTCGGTCAACTCGG
CCCAATTCCTCTACAACATCGAATTCCGCGGCAGGGGCGATATCAGATACTGAGTAGGTGGCAGG
AGTGGTATCAGCAATCCAGTATTGCAGCATTATACTATACTCTAAGAGAAAAAAAGGAAGCGATA
GAAAAGCGCCACCAGAACCAGATGATTGGAGAAGAAGATCCGGAGACAGATCTTGATTACTTGCC
GGTGGGCGCTCTCTTGGGTCTCCTGTGCTACCTCGACCAAAACCAAAAAGGGCTACACCCTCTGA
TTCCGGGACAGAATTTGTTGAAAATGATTCCACAGTCTCAGTTTT
Right flanking sequence: Indices 284934 -- 285433
TCCTCCGCGGCATCGGTGGTTACCACTGAATGGGATGTTGTCGCTTACTAGGATGTTTTCTCTTA
ATCGTCTATAGAGTTTCGAGCTAGTGATCACTAATTTCTTTGGCAGAAGCTTCGATCTAGAATGC
AGTATCCGGGATTTTCAAAGGATACCGCTCTAGGAGTAATCTCAAGTCCTTCCCTCCATTGCTTA
CGGAGACGGCAAATCCAGATCAAGTTCTAGGCCGGGTTGGCATCAATGTTAGCAGATCGACTCCA
AAGAATGCCGGGGAGTTGGAGAAGATTGAGTTCGTGCGATAAGAATCAGAGTCATGGCGGGGGAG
AGCCCCAAAGTCAGTGGAGTTAATGGGACGACTCCGCCTTCAATAAAGAGGAAGCAAGTAGGGCA
CAGGCTTTGAGGTTGGAGCCTTGCCCGTGAAGGTATCCCAATAGTTGTGCTAATCCAGACTAGAC
TGTCTTCCAGAAGCAAAAAGGAATCCTATCGCTATAAGAGGAAGT
Found at i:320729 original size:22 final size:22
Alignment explanation
Indices: 320687--320730 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
320677 CGAAAACACA
*
320687 TATGAAAGACCTATTCAATACC
1 TATGAAAGACCTATACAATACC
*
320709 TATGAGAAGCCCTATAC-ATACC
1 TATGA-AAGACCTATACAATACC
320731 ATAACGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (22 bp):
TATGAAAGACCTATACAATACC
Left flanking sequence: Indices 320187 -- 320686
CTGAATCGGGGCTCTCAACATTGGAGGAATTCATAGCCGGAAAAGGAATAGTCGTCTCAGTCTAG
TCGTCGAAAGGCAAGTCTTCAGAGATAGCATCCGCGCGATCAGCACTAAGTCCAGTCTCTGTCAA
AAGCAGAATCCTAGGTAGATAGTGATTCACCATACACATGAATGCCCGAGGAAAGTCTTGATCTT
GATTCATAGCTGCCCTAGAGTTCAAAATGAGCACATCCATCTAGTCAAGTTGATCTTCAGAGATG
GGCAGGGAATAAAGAGAATTCAATTTCCCCAAGGGACAATATCCAATAAATAGAAGAAGGAAGTC
TGCCCAAGGCATGTCAAAAATCTTTCCCGCTCTGGCTCCGCAAAGAAACTAGCTAAAACAGAGCT
CGCATGAATTGCTCGTAAAGAGGGCCTCATCTGCACCGACAGCAAGCCTTTCTACAGCGAAGGAA
ACAACTGGCCCGCCATCCAATACCTATTCTGCCCTCGAAAACACA
Right flanking sequence: Indices 320731 -- 321230
ATAACGATAGCATCTCAAAGTAATAACACTAGGTAATCTTCCTCAGAACGGGAATGCTAGACCCT
ACCAAGTAAAGCAACTCCAACTGTCACTGCAACAAGTTCGAAGGCAGAAGCAATTGAATCTGCAA
CTGGCTAGAAAACTCTTCCTTACAACCACAACCTATGGAAACTCCCCATGGCAGGGAGGATGACT
TGAAGGCAATCGTTGGTAACTATTGATTGAATTAGCATTACCTAGTAGTGCACTCAAGAATCTCG
TAGAATTTCCTCTTTTAGCTATTTATTAGAGGCCCTTCCATTTATCCCAGGTTTGAAATATCTGC
TTTGAAAGGACCAGGAAAAACAAAAGAGACGAGACCTTTTCTATTCTACGATCGGAGTTTGACTA
TCTGTAACGATAGGAGCATTAGTCAAACATATGAGTCATATTCAAGATTTCCCTATGGAAGGAAG
ACTAAGTATGAATGAAACTTCCTTTTTCCAGTTCTTTCTATACTA
Done.