Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3426
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 23185
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Found at i:13664 original size:34 final size:33
Alignment explanation
Indices: 13626--13720 Score: 129
Period size: 34 Copynumber: 2.8 Consensus size: 33
13616 GCGAATACAT
13626 TCTGGGCTTAAGCCCATATT-AGTAACAGTAGCAG
1 TCTGGGCTT-AGCCCAT-TTCAGTAACAGTAGCAG
*
13660 TCTGGGCCTTAGCCCATTTCAGTAACAGTAGCGG
1 TCTGGG-CTTAGCCCATTTCAGTAACAGTAGCAG
*
13694 TCTGGGCTTTAGCCCATTTCAATAACA
1 TCTGGGC-TTAGCCCATTTCAGTAACA
13721 TTAATCAATG
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
33 3 0.05
34 50 0.89
35 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (33 bp):
TCTGGGCTTAGCCCATTTCAGTAACAGTAGCAG
Found at i:13743 original size:18 final size:18
Alignment explanation
Indices: 13716--13753 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13706 CCCATTTCAA
*
13716 TAACATTAATCAATGCAG
1 TAACAGTAATCAATGCAG
*
13734 TAACAGTAATCAGTGCAG
1 TAACAGTAATCAATGCAG
13752 TA
1 TA
13754 TGCAAGCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (18 bp):
TAACAGTAATCAATGCAG
Found at i:14158 original size:27 final size:27
Alignment explanation
Indices: 14124--14242 Score: 145
Period size: 27 Copynumber: 4.5 Consensus size: 27
14114 TATTACAATT
*
14124 ATTTTACCCTACAGGGGTATTTAGGTC
1 ATTTTACCCTATAGGGGTATTTAGGTC
* * * *
14151 ATTCTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATAGGGGTATTTAGGTC
*
14178 ATTTTA-CCTATAGGGGTATTTTGGTC
1 ATTTTACCCTATAGGGGTATTTAGGTC
*
14204 ATTTTACCCTATAAGGGTATTTCA-GTC
1 ATTTTACCCTATAGGGGTATTT-AGGTC
14231 A-TTTACCCTATA
1 ATTTTACCCTATA
14243 AGGGCAAAAC
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
26 34 0.43
27 45 0.57
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTATAGGGGTATTTAGGTC
Found at i:14205 original size:53 final size:53
Alignment explanation
Indices: 14109--14242 Score: 164
Period size: 53 Copynumber: 2.5 Consensus size: 53
14099 TGTTACTTTA
* * *
14109 AGGGGTATTACAATTATTTTACCCTACAGGGGTATTTAGGTCATTCTACCCTAT
1 AGGGGTATTTC-ATCATTTTACCCTATAGGGGTATTTAGGTCATTCTACCCTAT
* * *
14163 GGGGGTATTTCGATCATTTTA-CCTATAGGGGTATTTTGGTCATTTTACCCTAT
1 AGGGGTATTTC-ATCATTTTACCCTATAGGGGTATTTAGGTCATTCTACCCTAT
*
14216 AAGGGTATTTCAGTCA-TTTACCCTATA
1 AGGGGTATTTCA-TCATTTTACCCTATA
14243 AGGGCAAAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
52 5 0.07
53 47 0.68
54 17 0.25
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (53 bp):
AGGGGTATTTCATCATTTTACCCTATAGGGGTATTTAGGTCATTCTACCCTAT
Found at i:14246 original size:26 final size:27
Alignment explanation
Indices: 14109--14242 Score: 141
Period size: 27 Copynumber: 5.0 Consensus size: 27
14099 TGTTACTTTA
* * * *
14109 AGGGGTATTACAATTATTTTACCCTAC
1 AGGGGTATTTCAGTCATTTTACCCTAT
*
14136 AGGGGTATTT-AGGTCATTCTACCCTAT
1 AGGGGTATTTCA-GTCATTTTACCCTAT
*
14163 GGGGGTATTTC-GATCATTTTA-CCTAT
1 AGGGGTATTTCAG-TCATTTTACCCTAT
**
14189 AGGGGTATTTTGGTCATTTTACCCTAT
1 AGGGGTATTTCAGTCATTTTACCCTAT
*
14216 AAGGGTATTTCAGTCA-TTTACCCTAT
1 AGGGGTATTTCAGTCATTTTACCCTAT
14242 A
1 A
14243 AGGGCAAAAC
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
26 35 0.39
27 55 0.61
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (27 bp):
AGGGGTATTTCAGTCATTTTACCCTAT
Found at i:14255 original size:26 final size:26
Alignment explanation
Indices: 14201--14260 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
14191 GGGTATTTTG
* ***
14201 GTCATTTTACCCTATAAGGGTATTTCA
1 GTCA-TTTACCCTATAAGGGCAAAACA
14228 GTCATTTACCCTATAAGGGCAAAACA
1 GTCATTTACCCTATAAGGGCAAAACA
14254 GTCATTT
1 GTCATTT
14261 CAACACATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (26 bp):
GTCATTTACCCTATAAGGGCAAAACA
Found at i:15348 original size:19 final size:20
Alignment explanation
Indices: 15324--15361 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
15314 GGTACCACCA
15324 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
15343 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
15362 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:15701 original size:93 final size:93
Alignment explanation
Indices: 15591--15761 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
15581 GCCCCTAAGT
* *
15591 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
15656 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
15684 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
15749 CGAGTTCGGATGC
66 CGAGTTCGGATGC
15762 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:15758 original size:46 final size:46
Alignment explanation
Indices: 15586--15758 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
15576 AACCCGCCCC
* * * *
15586 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
15632 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
15680 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
15725 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
15759 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Done.