Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: KC784958
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: 104131
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:2422 original size:20 final size:20
Alignment explanation
Indices: 2397--2436 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2387 GCAACATATA
2397 TTCTATTATATATTGCCGCG
1 TTCTATTATATATTGCCGCG
2417 TTCTATTATATATTGCCGCG
1 TTCTATTATATATTGCCGCG
2437 CCCCTTCAAC
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:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (20 bp):
TTCTATTATATATTGCCGCG
Left flanking sequence: Indices 1897 -- 2396
AGTCTCTGGATATTGAAGACCAGTTATTTTCCCTATCCAATAGTAGAATCCTGCAAATAAAGCAA
AAACAGCTCCCATAGAAAGAACATAATGGAAATGTGCAACCACATAATAAGTATCATGTAGAGCG
ATGTCCAGCCCAGAATTGGCCAATACTATTCCAGTGAGAGTAGAGTAGGTGCCCTTACTCGCGTG
GGGCCAATTTTGGGTTTCCCTTGCGCTTTTAGTGCACCTCTCTCGTAACCGTACATGATAGTTTT
CCCATCATACGGCTTGCCCGCGCGTTTAATTCTCTCACGACTTGGCACGGGTTTCATAGCCTGTA
CCGACGTGTCGAACGAGGCTGCGGTGCCTCTCCGGTTTCCTTTTTTTCCCTCTGAGTTTATCTTT
TCGATCGAAGAGAGAGAGCCCGAAGAAGTATTTTCCGTGGTCGGCTCTCTCGTGCTCGAGCTTGG
CAAGTGTAGCCAGAGAATAACGCGGCAGCAAGGGCGCAACATATA
Right flanking sequence: Indices 2437 -- 2936
CCCCTTCAACAACTTTCTCAGTTTCATGAGCTTTTAGTCTGGTCATCATCTCGTTTATCTGTGAG
ATGTTCTTGTCGAGTTGGCTCAACTTGCGCTGCTATTGTTGTGTCCTCTTTATTGGTCCGGATTT
GTTGACTAGGCATCTGGTATCGTCCAGTATAGATCTGCCGCGTAGCCTTTTGAAAAGAGGCGTAG
CGGGACCAAGCTTTTTGGTTGGGGTTTTCCAACATACTTGTGTGCTCTTCTTGTCTTGGTTCGGA
CTTCTATAACTGCAGAACACCAGAAAGTCACCTCTGACTTAATTCCGAGTTCCTTTCCCTGGAAA
ATGATGTTGATATATCACTTCTGGAGAAGCCTGCGGCCTCTTGTTTTAATCCGTCCCATTGTAGT
TGTAAGGCGTTTGCTTTTTTTAGTATGATTAGAGTGCGAACACAGCAGCTCCTGATGACGAGTTT
CATTTCATTTGTTAATTGGTAGAACTTATCAACGAACGAATAGTA
Found at i:18093 original size:17 final size:16
Alignment explanation
Indices: 18073--18108 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
18063 TTTTTTCTTC
*
18073 TTTTTTTTTTTTTCGAA
1 TTTTTTTATTTTTC-AA
18090 TTTTTTTATTTTTCAA
1 TTTTTTTATTTTTCAA
18106 TTT
1 TTT
18109 ATGGGAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTTTTATTTTTCAA
Left flanking sequence: Indices 17573 -- 18072
AAGGCTCCGCGCCTTCCAGGAGCTATGGCTACAGAAGTAGCGTACCGGGGGCGCAAAGCCTTCGC
CGAAGGCCGAAGAAGAGAAGCCTTCGGCCCTGCCAATGAATCATTTTTTTGTTTCAATTTTGAGT
TTTTTTATCTTGTATTCTTTTCTTCTTTAAAGCAAAATCCTAAAAACAAATAGAGCAGATGGTCC
AACTACAGAACTTTTTTTTTTTTCTTATGTTTATGGTTGTGCTTTGTGGTACGGCAGCACCCATA
CTATTTCAATGGTTGGTAAGTAGAGATGTTCCCACAGGTGCTCCTTTTTCTCATGGTACTATAAT
ACCTATTTTTACCTCTTTATTATTGCTTCTAGTTCATGTACATTCCAGGGGATTCATACGCTCTA
TGGAGAAAACAGAAAGGATAGTTTTGGTAAAAGCAAAACGCATTTTATTACTCAACATAATTGAA
AAAAGCTCCCCAAAAACTAGAGCTAAAAATGCATTTTTTTTCTTC
Right flanking sequence: Indices 18109 -- 18608
ATGGGAGACTTGTCATATTTAGAATCTTTCTGTAGTGTACTTTGTTTTTTATTATTTTGTACATT
TTTTTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAG
AGAAAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGA
AAAAAGAAACAAAGAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAA
AATATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTT
TGGCTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAAT
AGATTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGTCATGACTTTCGAAAAGT
TCCCATGACTATGAAAATTTCACATGGAGGAGTTTGCATCTTTAT
Found at i:18179 original size:21 final size:22
Alignment explanation
Indices: 18144--18186 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
18134 CTTTCTGTAG
* *
18144 TGTACTTTGTTTTTTATTATTT
1 TGTACATTGTTTTTTATCATTT
18166 TGTACATT-TTTTTTATCATTT
1 TGTACATTGTTTTTTATCATTT
18187 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 17644 -- 18143
CCGAAGAAGAGAAGCCTTCGGCCCTGCCAATGAATCATTTTTTTGTTTCAATTTTGAGTTTTTTT
ATCTTGTATTCTTTTCTTCTTTAAAGCAAAATCCTAAAAACAAATAGAGCAGATGGTCCAACTAC
AGAACTTTTTTTTTTTTCTTATGTTTATGGTTGTGCTTTGTGGTACGGCAGCACCCATACTATTT
CAATGGTTGGTAAGTAGAGATGTTCCCACAGGTGCTCCTTTTTCTCATGGTACTATAATACCTAT
TTTTACCTCTTTATTATTGCTTCTAGTTCATGTACATTCCAGGGGATTCATACGCTCTATGGAGA
AAACAGAAAGGATAGTTTTGGTAAAAGCAAAACGCATTTTATTACTCAACATAATTGAAAAAAGC
TCCCCAAAAACTAGAGCTAAAAATGCATTTTTTTTCTTCTTTTTTTTTTTTTCGAATTTTTTTAT
TTTTCAATTTATGGGAGACTTGTCATATTTAGAATCTTTCTGTAG
Right flanking sequence: Indices 18187 -- 18686
AAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGAAAAGAAAACC
GCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAAAAGAAACAAA
GAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAAAATATTTTTGATT
TATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGGCTTTTTATTC
TCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGATTTTTTATTG
TTCGCGCCTTACCGAAAAGACTGATGGATGTTGGTCATGACTTTCGAAAAGTTCCCATGACTATG
AAAATTTCACATGGAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGC
TTATGCGCGACCATCTCGTGTTTAAGCTCACGCCATGTGGGCGTG
Found at i:18589 original size:19 final size:20
Alignment explanation
Indices: 18547--18589 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18537 GGATGTTGGT
* *
18547 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18567 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18586 CATG
1 CATG
18590 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 18047 -- 18546
GAGCTAAAAATGCATTTTTTTTCTTCTTTTTTTTTTTTTCGAATTTTTTTATTTTTCAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTAGTGTACTTTGTTTTTTATTATTTTGTACATTTTT
TTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGA
AAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAA
AAGAAACAAAGAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 18590 -- 19089
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCTCAAATTAGTGCAAG
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAATGCCAGGCCGCGGGTAACGCTAGTTGGCTCC
CAGGCGTTAAGCATTCCTAACAATACGGAAAAAGAGGTCGTGATGATATTCATCTACGTTCGTAC
TGTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAG
TTCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAA
Found at i:41040 original size:81 final size:81
Alignment explanation
Indices: 40905--41054 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
40895 AAAATACTCG
*
40905 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
40970 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
40986 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41050 CCAAG
65 CCAAG
41055 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 40405 -- 40904
CAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTGGAAATAACATC
AGTATTTCAACAACTTTTTGAGCTCATTTTTCACCCATATAATTCTTTATGTTTTTGTTTGAACA
AGCCAATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGG
ATAACCACTTAGTAACTAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTAACAG
AACTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTAATATTTTGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTTCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41055 -- 41554
TGAGCTTAAGGAAACGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCTAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCGTTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTCATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTGTATTTAGAACTAAAAGAAAA
TAATGCTTTTTTAGAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATAGAATATAGTAGAAAATAATAAGTTGGCGAGGAAGTAAAAATATATA
TATATATCTATAGATATATATATATTTTTTTTTTATTCTGTGGAT
Found at i:62924 original size:14 final size:14
Alignment explanation
Indices: 62905--62932 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
62895 TCTTCGTTTT
62905 TATAAGATATGAAG
1 TATAAGATATGAAG
62919 TATAAGATATGAAG
1 TATAAGATATGAAG
62933 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 62405 -- 62904
AGAGGCTGTTAAGATAGCTGCTAATGCCATAGGCGCGTTTACTGCGGCGGGGTACTTGGTTGTAC
GTGCACAATTTAAATAGAGCGAATGCATTAGAATTGTAAGAAAAAAGCCTAAAATTGAAAAAGCT
AAAGTTCAATTATAAGGTACTTATTAATGAAGCTAAAAACACGGATCAGCTTTTGGAAGAAATTG
AAGAGCGTTAAATGAAAGAAATTAAGGCTTGTTGGTTGGGTAGTAAAAAAAATGAGTACTGATGA
AGAATGAACAGCCACGTCTAGATGATGCTGTTTAGCGTGTAGTAGAAGCTAAATACAACAAGCTG
CAAGCTAAGGGTAAGGGTCTTCGCGCGACAAGATTCGAGATCAGTATGCGGAACAAACGACCATA
AAAGAAAGGCCACGAGTATCATAGGCAGACCTTCAACAGGCACCTAAAAAAAAATTACCACCTAA
ATTATCTATTAAGTACCCTGTCCCAAACGCAAACTTCTTCGTTTT
Right flanking sequence: Indices 62933 -- 63432
GTATTTTTGTTTCTCGAAGAGCCATCGGGAACTTAGGTTCTTTTATTTATCGAGTTTCGCAAGTA
TATCTTTCTTAGGATCTAAATCCTATTAATTTGAACGTAGAGTTGTATGATGCGAAACTATCACT
TACGGGGTGGGTTTAATCTTAGATTTTTTTATTTTCTGAGTTTTTATGGGATTATTATCGCGGGT
TTGTCTATCCTAATGGGCGTCTAACAAAAAAATCGATTTTTTTGTTGGTTGGCCCTTTTGTGGGG
CCTGTTGAAGGGCCGAAGTAGTTCTGAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACA
TGGCTATTTCCAATTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGC
AACACCTATGATGCAAGGAATAATTGAGTGCGCCTAGATATATCATCACGGTTGCAGAGCTCTGC
TCCAACTCTGCCATATCTGCTCGAGCTGGCTATCGCCAGGATGTG
Found at i:103993 original size:10 final size:10
Alignment explanation
Indices: 103978--104003 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
103968 TCTTCTTATA
103978 AATAATCTTT
1 AATAATCTTT
103988 AATAATCTTT
1 AATAATCTTT
103998 AATAAT
1 AATAAT
104004 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 103478 -- 103977
TCTATCGGGGGGGGGGGAGTTGTGCATCATAGGTACCTTCTTATTGCTGCGAAGGGCGATATGAA
AATAACCCCCCTATCCAACCTCATTCTGTTGCGCGAAATCCATCATTGGCTAAGCAATTATTTGG
TTATGCCATCTTAGGTTTCGCTTTAACAGAAGCTATTGCTTTGTTTGCCTTAATGATGGCCTTTT
TGATCTTATTTGTTTTTTAATTTTTTGGTGCTGCGATTTTTTGGGAAAAAACTCTATTTTGGCCG
CACCCTATTGGCTTTGCGAATAGGGCTGCGCCCAAAAAATCTAGATTTTTTGGCACCTTAGGGCC
GAACGATTAGTACGTTCGAGCCCTTCACCACTTGCTACCAAAAGCATAAGCGTAAAAAAACTGAA
CTGACAAAGATTTTAACCTTAAAGGCTCATTGGATAAAAAAAGAAGCAGGACAAATATATCTATA
TATATATTTTTTTTTTCTTTTTTAGCTGCTTCACTTCTTCTTATA
Right flanking sequence: Indices 104004 -- 104131
GCATAGCTTCGCGTGCTTTTCGATTGATGATGGGACCGAAGACGAAAGGCGCGAAGCGGCCGCGG
GTCTAGATTCTCGTTTTTTCGGCCGCGCGCCTGCGGCGGCCCTCGGTCGTTGTTAACTTACCA
Done.