Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_046759
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: 117857
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:20517 original size:19 final size:20
Alignment explanation
Indices: 20475--20517 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
20465 GGATGTTGGT
*
20475 CATGACTTTCGAAAAGTTTC
1 CATGACTATCGAAAAGTTTC
20495 CATGACTAT-GAAAA-TTTC
1 CATGACTATCGAAAAGTTTC
20513 ACATG
1 -CATG
20518 TAGGAGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 9 0.43
20 8 0.38
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
CATGACTATCGAAAAGTTTC
Left flanking sequence: Indices 19975 -- 20474
TTTTATTTCTTATTTTCATTTTTAATTCTTTTATTCCCAAATTTATGGGAGACTTGTCATATTTA
GAATCTTTCTGTGGTGTGTTTTGTTTTTTATTATTTCGTACATTTTTTCTATTATCTAAATATAG
GCACGATGGGTTAGCAAACAAAGGGCGTAGGCTTGGGATGGAGGAGATGAAAGCGCGTAAGCGGG
CACAGGAAATAAAGCGCCAAGCGATTTGGCCTAACGAGAGGAAGAAACAAAAAAATGAAAAGAGA
GAAATTTTTTATTTTTTATTTTTTTTAAATAAATCAAAAATATTTTTGATTTATTTGCTGCGATT
TTCAAAAACCTTCGGCCTGAACGAAAAAGCCAAAATTTTGGCTTTTTATTCTTTGCTTGCTTTTT
CGCAAGCTTATTCTTTCGTCCCTGAAAATAAAGCGCAAAGCGCCAAGCGCTTTGATTGGAATAGA
TTTTTTATTGTTCGCGCCTCACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 20518 -- 21017
TAGGAGTTTGTATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGTGGCTTATGTACGATCA
TCATCGCTTCTAAGCCCACGCTGTGTAGGCGTGAACTCTGGTTGAATTCGGGTTTTAAATCCCGC
CGCTGAGATGCTCAGTTGACTCTTGAACCTTGATAAGAAGACGGCTTCTTCCCAAATTAGTGCAA
AAGGTTTAAGGACTTGGGATGAACTAATGTGAATGGGTATAAGCTTCGCTCCTCAAAAACACCCA
GTACTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCAAAG
TGGCGTTAAGCATTCCTAGCGGTACGAAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
CTCCTCGTGGAGTAAATCCCACATCCAACCATCTAACCAGGGAACGAGATAATTCCCACTAAGTT
CCAGTAAAACTGGCAGGCCAGCCGAGCTATAAGCTAGTGGGAACA
Found at i:31469 original size:2 final size:2
Alignment explanation
Indices: 31462--31530 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
31452 GGAAACAAAA
* *
31462 AT AT AT AT AT AC AT AT AT AT A- AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
31503 AT CT AT AT AC AT AT AT A- AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31531 ATTTTTTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 30962 -- 31461
GATAATTATAGATTCTTTTAAGAAACAAAAAACAAAAAAACATATTTGATAATTATTAAACAAAA
TACTCTGAAAAGAATCAAGATCCACTTTCGTGTCATTTCGTGGTGAACATAATCCGTCAGAATCT
CTTCGATTCCCACATGAATATGCCAGAATACCAAGATATTTAACAGAATCAGAGTGGAAACATTT
GCTATAAGAATGGTTGGGATTAGAAAAGCGGCAGTCATTCTTTGAAGAAGCCAATGCCCTAAGGT
TTCTCTATGAGCTTTCATTGCTTTTCACCTTTTTTTTCCGAGAGTAAGACGAAAGCGGCCTTTTT
TGTTCGGGCCCCAGAAGCTTATGTAACAGTCGCCCGTCATATGGCTCCGCTTATCAAAAAGTAGC
CTGTCGGCTGAAATAGTACTACGACAGGTTGTAGACTCGTCTGAGTTAACCCTGCGCGAGATAAA
GTGGACCCAATTACGAAGCATTGCAGAGCCAATCAGGAAACAAAA
Right flanking sequence: Indices 31531 -- 32030
ATTTTTTATCTATATCAATATATAATATATGTATAATTCTTTTTTGCTTCGCGCCTTTAGTTATA
GTTATTTTGAACCCGTTTCGACCGTTCCCACCATATTATTCCAGGCATTGATTAGACTGGGTCGT
AGAGGGCGCAGGCAGCGTCCTCACGTCCTTCAGGGTCATCCATTCTGTGGGGGTCGGAACGGTGC
ACATGTGACGAAAACGGTCTACACTCCGCGCCTTTGGGTTGCGACGAATATAAGCCAAAAAAATA
TATTTTTTTCGCCTCTAACGAGTATCGTACTCTGCGCTTACGAGAAATAGAATCGGATAATGTTC
AATACAGCTAAACAAGCTGCACAGAACAACATAATAATTCCGGAAGTATATACTTTGGATAATTC
TAGAAAAAAACCCAGATCCCACAATAAATGACGAATTCCATTACTCATATGATAGCACAACGCTA
ATAAAGTGAAATTGACTACGCTTAGAATTAACCAATGAAAGTAGA
Found at i:31541 original size:35 final size:36
Alignment explanation
Indices: 31502--31573 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 36
31492 TATATATATA
31502 TATCTATAT-ACATATATAATATATGTATAATT-TTT
1 TATCTATATCA-ATATATAATATATGTATAATTCTTT
31537 TATCTATATCAATATATAATATATGTATAATTCTTT
1 TATCTATATCAATATATAATATATGTATAATTCTTT
31573 T
1 T
31574 TTGCTTCGCG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 30 0.86
36 5 0.14
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (36 bp):
TATCTATATCAATATATAATATATGTATAATTCTTT
Left flanking sequence: Indices 31002 -- 31501
CATATTTGATAATTATTAAACAAAATACTCTGAAAAGAATCAAGATCCACTTTCGTGTCATTTCG
TGGTGAACATAATCCGTCAGAATCTCTTCGATTCCCACATGAATATGCCAGAATACCAAGATATT
TAACAGAATCAGAGTGGAAACATTTGCTATAAGAATGGTTGGGATTAGAAAAGCGGCAGTCATTC
TTTGAAGAAGCCAATGCCCTAAGGTTTCTCTATGAGCTTTCATTGCTTTTCACCTTTTTTTTCCG
AGAGTAAGACGAAAGCGGCCTTTTTTGTTCGGGCCCCAGAAGCTTATGTAACAGTCGCCCGTCAT
ATGGCTCCGCTTATCAAAAAGTAGCCTGTCGGCTGAAATAGTACTACGACAGGTTGTAGACTCGT
CTGAGTTAACCCTGCGCGAGATAAAGTGGACCCAATTACGAAGCATTGCAGAGCCAATCAGGAAA
CAAAAATATATATATACATATATATAATATACATATATATATATA
Right flanking sequence: Indices 31574 -- 32073
TTGCTTCGCGCCTTTAGTTATAGTTATTTTGAACCCGTTTCGACCGTTCCCACCATATTATTCCA
GGCATTGATTAGACTGGGTCGTAGAGGGCGCAGGCAGCGTCCTCACGTCCTTCAGGGTCATCCAT
TCTGTGGGGGTCGGAACGGTGCACATGTGACGAAAACGGTCTACACTCCGCGCCTTTGGGTTGCG
ACGAATATAAGCCAAAAAAATATATTTTTTTCGCCTCTAACGAGTATCGTACTCTGCGCTTACGA
GAAATAGAATCGGATAATGTTCAATACAGCTAAACAAGCTGCACAGAACAACATAATAATTCCGG
AAGTATATACTTTGGATAATTCTAGAAAAAAACCCAGATCCCACAATAAATGACGAATTCCATTA
CTCATATGATAGCACAACGCTAATAAAGTGAAATTGACTACGCTTAGAATTAACCAATGAAAGTA
GAAAGTGGAAAAAAAAGCATACCGGTAAAAATAATAAGAAGTAAG
Found at i:42523 original size:20 final size:20
Alignment explanation
Indices: 42498--42537 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42488 TGTTCGCCTG
42498 GGTTTAGAACGTCGTGAGAC
1 GGTTTAGAACGTCGTGAGAC
42518 GGTTTAGAACGTCGTGAGAC
1 GGTTTAGAACGTCGTGAGAC
42538 AGTTCGGTTC
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:0.35, T:0.25
Consensus pattern (20 bp):
GGTTTAGAACGTCGTGAGAC
Left flanking sequence: Indices 41998 -- 42497
GTCTGAACTTCCAGTAAACTGGAAGCCTAAAGCACTGTTCACTACAAAACAGTGATAGGACATTC
AAACTGCTAATAATAACATACAAAAAGTTAACAAAATGACTATATGTAGAAGAAAAAGAATAGAA
ATACTGAAGCAAGCACTTCAACTGAATCAGATACAACGACAAGTATGTTGCAGAGTGGATGAACA
TAATTGCCTAAAGAGTAACGGAGGTGTGCGAAGGTAGGCTCAAGCTAATATTCTGACAGCTTTAG
AGCGTAATGGTACAAGCCTGCCTGACTGTGAGACTTACCAGTCGAACAGAGACGAAAGTCGGCCA
TAGTGATCCGGGAGTCCCGTGTGGAAGGGCTCTCGCTCAACGGATCAAAGGTACGCCGGGGATAA
CAGGCTGATGACTCCCAAGAGCTCTTATCGACGGAGTCGTTTGGCACCTCGATGTCGACTCATCA
CATCCTGGGGTTGAAGAAGGTCCCAAGGGTTCGGTTGTTCGCCTG
Right flanking sequence: Indices 42538 -- 43037
AGTTCGGTTCCTATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACCCTAGTACGAGA
GGACTGGGTTGGGTCAACCTATGGTGTACCGGTTGTTATGCCAATAGCAGCGCCGGGTAGCTAAG
TTGGTATAGAAGAACTGCTGAAAGCATCTAAGCGGGAAATCCTTCTCTATACAAGTTCTCATAAA
AGGTGAAAGACCATCACTTTGATAGGCGAGAGGTGTAAACACCGTGAGGTGTGAAACAAGGCCTA
CGGCTCTTGTTCAGCTTACTCGTACTAATTATCTACTTTCTGTTCCTTCTGTGCGAGGCGCAAAG
ATGTAAGATTAATACTTGTTTTCGTCAGGGGTTCGGAGACCTGCCCCGCCCCTTCGGGGGCAGGG
AGCCCATGGCTCTCCGGAGAGAACCAGAAATTGTTGCGATCTGGTTTAAGGAAAGTAAAAAAAAA
ATTTATCATAGAATATTGTTATAAAAAAAGGCTATTCACTTTCCT
Found at i:48207 original size:81 final size:81
Alignment explanation
Indices: 48072--48221 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
48062 AAGATACTCG
*
48072 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
48137 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
48153 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
48217 CCAAG
65 CCAAG
48222 TGAGCTTGGG
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 47572 -- 48071
CAACAACTTTTTGAGCTTATCTTTTATCCATATAATTCTTTATGTTCTTGTTTGAACCAGCCAAT
ACGAGCAGAGTGATCCATCAGCAAACATGGCTGATGATGTCCAAGAAGCGTGGGCGCAATGTCTA
ACGCCCCACCCCTTTATGCTTCATCCGCTATACGAAAAAAAACGGGAGGATCCAATAGGGTTACT
TAGTCACCAGGGGATAACCACCCAGTAACTGGGGGCCATTTTGCCAATCAAGGCCGCAGGCTTGA
TTGACAAAGCTGGGGCACGTAGTTTACAGCGAAGCTTCTTTTTCCAAAATATTTTGGAAAATCCC
CAAAAAATATTTTTTGCGCAGCGCCCTCGAAGATTGTAAAGATTCAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATATTCGCCCTTTCTCTCGATTCAGACATTAAGATACTCG
Right flanking sequence: Indices 48222 -- 48721
TGAGCTTGGGAAAGCGAAGCGCAGAGCGGAGACATAATCCTTTCTGTTTCGTTTTTTTTTTTGCC
ATTTCGTTCTTTAGACACCGCAGCTTGGCCAGACCTGCGGCATTTCTTCAAATATTTGAAAAAAT
ATATATTTTGCTGCGCCCTCTACCCTAAGGCGTGTAGAGCCCTCTCTTTATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGACTCAATTTAGTCGTCGCAAAAGCCTTGGCAA
TGGCAATGACTTTTGTACGACATGCATAATACTCCAATAAAAAGGTAAGCCTCTCTTGACTCTAT
CTAGAATTGGAAGAAGAGAATGCTTTTCTTCGCTGACGGCTGAAGAAAAGCAATGAAGTGCAAAA
AGGGTTGGAATAAAAAATGCATAGCAAAAAAAATTTTGAGCTTTGTTCTATGTGGTTTCGCTATC
TAGATAATATAATGTAATAAGAAATAATCAGTTGGCAAAGAAGTA
Found at i:69516 original size:15 final size:15
Alignment explanation
Indices: 69496--69526 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
69486 CAGGTCGGAA
69496 AAAGAAATATATTAT
1 AAAGAAATATATTAT
69511 AAAGAAATATATTAT
1 AAAGAAATATATTAT
69526 A
1 A
69527 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
AAAGAAATATATTAT
Left flanking sequence: Indices 68996 -- 69495
TTGATTGTACTTAAAGCAAATAACCAAACCCTTTGTAGGCTCTGTTTTTTACATATGATTTTCAC
GGTTAACAAGAGAATCATACTGATCATGTGGAACAGATGCGGTTGTGCCGAGCACTCATAATGGA
TTTCGCCACGAGATGTATGATGCATTGTGTTTAGCTTGCTTGTAGCTATCCAGCTAGGCGCGTAG
GCGGATGAACTTGCTACACCCGATTGCTTGACTTGTTGTTTTGTCCATAGCACAAAAAATGACTT
AAAGCGATCGTAAGTGAGGACCTCCTCTATCCGAACAATTCAGGAACGCCCCCCTGGCACGCTTA
ATTAAGCACCGAAGGCCCATAAGACGCAACCCCGGCGGGGCTCGCTTCTTTTCCAAAAGCCCTTA
AATTTTTTTTATATTTCTTCTTCTTCGGACCTTTATTCAAGAATGAGCTATGGGAAAAAAGTGGG
TAAATCCGGGCCTAAAGTTCCCGCAAAGCGGGGGACAGGTCGGAA
Right flanking sequence: Indices 69527 -- 70026
TATATATATATATATATATATATATATATGCCGCACTCCGCGGCCTGGTGCTATCGGAATGTTAG
AGCCATCAGCAATGGCGTCAGAGTTTTTATAGCACAATGAATTGGAAGGGAAACAATCAGTTTTT
TAATCATTATGCAGTCATGGTATGAACTTGGTCTTCATAAAAGCAGAAAAAAAAATATTTTTTTA
GTTTAATTTGGCTGATAAACACCATCCATCATATTTGTTCAATTATGCTAGTTCCAAATACCGAG
CAAGAGCCATGTGCTCGGAAATCTTGCAAGCACGGTTCTCAGGGGAGCGTTTTGAAGGATTATAT
CATGGTGGGTTTGACTCAATAACTGCGATGTTGTACATGAGGGCAATTTATGTATGACTTGCTTT
CATCAAGTATCTTGCATGATTATTGAAGCCTAACATCATGGCCCATTATTATTCCAAAAAGCTTA
CTCTATGCATTGGGTCGTTGGTTCGAATCCAACCTAGAGAGTTAA
Found at i:69522 original size:2 final size:2
Alignment explanation
Indices: 69517--69555 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
69507 TTATAAAGAA
69517 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69556 GCCGCACTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 69017 -- 69516
AACCAAACCCTTTGTAGGCTCTGTTTTTTACATATGATTTTCACGGTTAACAAGAGAATCATACT
GATCATGTGGAACAGATGCGGTTGTGCCGAGCACTCATAATGGATTTCGCCACGAGATGTATGAT
GCATTGTGTTTAGCTTGCTTGTAGCTATCCAGCTAGGCGCGTAGGCGGATGAACTTGCTACACCC
GATTGCTTGACTTGTTGTTTTGTCCATAGCACAAAAAATGACTTAAAGCGATCGTAAGTGAGGAC
CTCCTCTATCCGAACAATTCAGGAACGCCCCCCTGGCACGCTTAATTAAGCACCGAAGGCCCATA
AGACGCAACCCCGGCGGGGCTCGCTTCTTTTCCAAAAGCCCTTAAATTTTTTTTATATTTCTTCT
TCTTCGGACCTTTATTCAAGAATGAGCTATGGGAAAAAAGTGGGTAAATCCGGGCCTAAAGTTCC
CGCAAAGCGGGGGACAGGTCGGAAAAAGAAATATATTATAAAGAA
Right flanking sequence: Indices 69556 -- 70055
GCCGCACTCCGCGGCCTGGTGCTATCGGAATGTTAGAGCCATCAGCAATGGCGTCAGAGTTTTTA
TAGCACAATGAATTGGAAGGGAAACAATCAGTTTTTTAATCATTATGCAGTCATGGTATGAACTT
GGTCTTCATAAAAGCAGAAAAAAAAATATTTTTTTAGTTTAATTTGGCTGATAAACACCATCCAT
CATATTTGTTCAATTATGCTAGTTCCAAATACCGAGCAAGAGCCATGTGCTCGGAAATCTTGCAA
GCACGGTTCTCAGGGGAGCGTTTTGAAGGATTATATCATGGTGGGTTTGACTCAATAACTGCGAT
GTTGTACATGAGGGCAATTTATGTATGACTTGCTTTCATCAAGTATCTTGCATGATTATTGAAGC
CTAACATCATGGCCCATTATTATTCCAAAAAGCTTACTCTATGCATTGGGTCGTTGGTTCGAATC
CAACCTAGAGAGTTAAATCGGCAGTAAGCTGCGCCCTCGTATCAT
Done.