Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1889
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: 26840
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4803 original size:26 final size:26
Alignment explanation
Indices: 4774--4881 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
4764 TGGTACAAAT
4774 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
4800 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
4826 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
4852 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
4878 TGAT
1 TGAT
4882 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:8782 original size:24 final size:25
Alignment explanation
Indices: 8737--8783 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
8727 ATTTTTGATT
*
8737 TTGATGAATATTTTGAGTTATGTCA
1 TTGATGAATATTTTGAGCTATGTCA
8762 TTGATGAATA-TTTGAGCTATGT
1 TTGATGAATATTTTGAGCTATGT
8784 GTTGTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (25 bp):
TTGATGAATATTTTGAGCTATGTCA
Found at i:9447 original size:45 final size:45
Alignment explanation
Indices: 9386--9506 Score: 127
Period size: 45 Copynumber: 2.7 Consensus size: 45
9376 TAGGATTCCA
* *
9386 ATATGTGTTTTTGTGTAAGACCATCTCTGGGACGTTGGCATCAAT
1 ATATGTGTTTTCGTGTAAGACCATCTCTGGGACATTGGCATCAAT
* * *
9431 ATATGTGTTTTCGTGTAAGACCA-CATTTGAGACATTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCATC-TCTGGGACATTGGCATCAAT
* * * * * *
9476 ATATTTGGTTACATATAAGACCATGTCTGGG
1 ATATGTGTTTTCGTGTAAGACCATCTCTGGG
9507 TCATCAGCAT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 1 0.02
45 60 0.98
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCATCTCTGGGACATTGGCATCAAT
Found at i:10336 original size:16 final size:16
Alignment explanation
Indices: 10312--10361 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
10302 GCTTAACTTC
*
10312 TATGCTTGAATTTGGT
1 TATGTTTGAATTTGGT
*
10328 TATGTTTGAATATGGTT
1 TATGTTTGAATTTGG-T
*
10345 TAAGTTT--ATTTGGT
1 TATGTTTGAATTTGGT
10359 TAT
1 TAT
10362 AATGCTACGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 3 0.11
15 5 0.18
16 13 0.46
17 7 0.25
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (16 bp):
TATGTTTGAATTTGGT
Found at i:14101 original size:27 final size:27
Alignment explanation
Indices: 14027--14304 Score: 310
Period size: 27 Copynumber: 10.4 Consensus size: 27
14017 TATTATGATC
*
14027 ATTTTACAAATC-GGGGTATTTCGGTA
1 ATTTTACAAACCGGGGGTATTTCGGTA
* *
14053 GTCTTACAAA-CGGGGGTATTTCGGTA
1 ATTTTACAAACCGGGGGTATTTCGGTA
* * *
14079 GTCTTACAAACCGGGGGTATTTCGATA
1 ATTTTACAAACCGGGGGTATTTCGGTA
**
14106 ATTTTACAAACTAGGGGTATTTCGGTA
1 ATTTTACAAACCGGGGGTATTTCGGTA
* ** *
14133 ATCTTACAAACTAGAGGTATTTCGGTA
1 ATTTTACAAACCGGGGGTATTTCGGTA
** *
14160 ATTTTACAAA-TTGGGGTATTTCAGTA
1 ATTTTACAAACCGGGGGTATTTCGGTA
*
14186 ATTTTACAAATCGGGGGTATTTCGGTA
1 ATTTTACAAACCGGGGGTATTTCGGTA
* * * *
14213 AGTTTACAAATCGAGGGTATTTTGGTA
1 ATTTTACAAACCGGGGGTATTTCGGTA
* *
14240 ATCTTACAAACCGGGGGTATTTCGATA
1 ATTTTACAAACCGGGGGTATTTCGGTA
* * *
14267 ATTTTATAAACTGAGGGTATTTCGGTA
1 ATTTTACAAACCGGGGGTATTTCGGTA
14294 ATTTTACAAAC
1 ATTTTACAAAC
14305 AAAGGTCTTA
Statistics
Matches: 217, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
25 1 0.00
26 55 0.25
27 161 0.74
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (27 bp):
ATTTTACAAACCGGGGGTATTTCGGTA
Found at i:14193 original size:107 final size:107
Alignment explanation
Indices: 14041--14304 Score: 350
Period size: 107 Copynumber: 2.5 Consensus size: 107
14031 TACAAATCGG
* * * * *
14041 GGTATTTCGGTAGTCTTACAAACGGGGGTATTTCGGTAGTCTTACAAACCGGGGGTATTTCGATA
1 GGTATTTCGGTAATTTTACAAACTGGGGTATTTCGGTAATTTTACAAACCGGGGGTATTTCGATA
* *
14106 ATTTTACAAACTAG-GGGTATTTCGGTAATCTTACAAACTAGA
66 AGTTTACAAA-TAGAGGGTATTTCGGTAATCTTACAAACCAGA
* * * *
14148 GGTATTTCGGTAATTTTACAAATTGGGGTATTTCAGTAATTTTACAAATCGGGGGTATTTCGGTA
1 GGTATTTCGGTAATTTTACAAACTGGGGTATTTCGGTAATTTTACAAACCGGGGGTATTTCGATA
* * * *
14213 AGTTTACAAATCGAGGGTATTTTGGTAATCTTACAAACCGGG
66 AGTTTACAAATAGAGGGTATTTCGGTAATCTTACAAACCAGA
* *
14255 GGTATTTCGATAATTTTATAAACTGAGGGTATTTCGGTAATTTTACAAAC
1 GGTATTTCGGTAATTTTACAAACTG-GGGTATTTCGGTAATTTTACAAAC
14305 AAAGGTCTTA
Statistics
Matches: 135, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
106 2 0.01
107 111 0.82
108 22 0.16
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (107 bp):
GGTATTTCGGTAATTTTACAAACTGGGGTATTTCGGTAATTTTACAAACCGGGGGTATTTCGATA
AGTTTACAAATAGAGGGTATTTCGGTAATCTTACAAACCAGA
Found at i:23536 original size:38 final size:37
Alignment explanation
Indices: 23474--23553 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 37
23464 TTATTACGAA
* * *
23474 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
23511 GTCTTACCCGGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCC-GGACAAAATCCCCACACGAAGTCATCGG
23549 GTCTT
1 GTCTT
23554 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 9 0.24
38 29 0.76
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:23825 original size:45 final size:47
Alignment explanation
Indices: 23671--23982 Score: 503
Period size: 45 Copynumber: 6.7 Consensus size: 47
23661 GCCCTTCGGG
*
23671 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
23721 AC-TTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
23769 ACTTTCACATTCATCACATCGG-CATTA-GCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
23814 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
23861 ACTTTCACATTCATCACATCGGCC-TTAGG-ATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
23906 ACTTTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
23952 AC-TTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
23983 ACACTATCAT
Statistics
Matches: 253, Mismatches: 3, Indels: 16
0.93 0.01 0.06
Matches are distributed among these distances:
44 3 0.01
45 87 0.34
46 38 0.15
47 51 0.20
48 52 0.21
49 20 0.08
50 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:23901 original size:92 final size:93
Alignment explanation
Indices: 23671--23981 Score: 497
Period size: 92 Copynumber: 3.3 Consensus size: 93
23661 GCCCTTCGGG
*
23671 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC-TTCACATTCATC
1 ACTT-TCACATTCATCACATCGGCCATTAGG-CTTATCAC--ATATATACACTTTCACATTCATC
*
23735 ACATCGGCCATTAGGCCCTATCACATATATATAC
62 ACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
23769 ACTTTCACATTCATCACATCGG-CATTAGCCTTATCACATATATACACTTTCACATTCATCACAT
1 ACTTTCACATTCATCACATCGGCCATTAGGCTTATCACATATATACACTTTCACATTCATCACAT
23833 CGGCCATTAGGCCTTATCACATATATAC
66 CGGCCATTAGGCCTTATCACATATATAC
*
23861 ACTTTCACATTCATCACATCGGCC-TTAGGATTATCACATATATACACTTTCACATTCATCACAT
1 ACTTTCACATTCATCACATCGGCCATTAGGCTTATCACATATATACACTTTCACATTCATCACAT
23925 C-GCCATTAGGCCTTATCACATATATAC
66 CGGCCATTAGGCCTTATCACATATATAC
23952 AC-TTCACATTCATCACATCGGCCATTAGGC
1 ACTTTCACATTCATCACATCGGCCATTAGGC
23982 CACACTATCA
Statistics
Matches: 204, Mismatches: 6, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
90 21 0.10
91 33 0.16
92 69 0.34
93 11 0.05
94 35 0.17
95 7 0.03
96 6 0.03
97 18 0.09
98 4 0.02
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (93 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCTTATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATAC
Found at i:23959 original size:137 final size:140
Alignment explanation
Indices: 23671--23982 Score: 508
Period size: 137 Copynumber: 2.2 Consensus size: 140
23661 GCCCTTCGGG
23671 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACACTTCACATTCATCA
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATATACACTTCACATTCATCA
* *
23736 CATCGGCCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCATTAGCCTT
64 CATCGGCCATTAGGCACTATCACA-ATATATACACTTTCACATTCATCACATCGCCATTAGCCTT
23801 ATCACATATATAC
128 ATCACATATATAC
*
23814 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATACACTTTCACATTCATCAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATACAC-TTCACATTCATCAC
*
23878 ATCGGCC-TTAGG-ATTATCAC-ATATATACACTTTCACATTCATCACATCGCCATTAGGCCTTA
65 ATCGGCCATTAGGCACTATCACAATATATACACTTTCACATTCATCACATCGCCATTA-GCCTTA
23940 TCACATATATAC
129 TCACATATATAC
23952 AC-TTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
23983 ACACTATCAT
Statistics
Matches: 163, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
137 63 0.39
138 20 0.12
139 6 0.04
140 15 0.09
141 21 0.13
142 34 0.21
143 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (140 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATACACTTCACATTCATCACA
TCGGCCATTAGGCACTATCACAATATATACACTTTCACATTCATCACATCGCCATTAGCCTTATC
ACATATATAC
Done.