Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2072
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: 50416
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Found at i:12332 original size:66 final size:67
Alignment explanation
Indices: 12203--12332 Score: 174
Period size: 66 Copynumber: 1.9 Consensus size: 67
12193 GGGATGTATC
*
12203 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
12268 AGGACA
62 AGGACA
* *
12274 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
12333 TTCACCATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.16
68 1 0.02
71 21 0.38
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:23929 original size:28 final size:30
Alignment explanation
Indices: 23856--23937 Score: 125
Period size: 29 Copynumber: 2.8 Consensus size: 30
23846 GAATATAATA
* *
23856 TGATTTGAGCCTAATGGGCCATA-AGAATG
1 TGATTTGGGCCTAGTGGGCCATATAGAATG
23885 TGATTTGGGCCTAGTGGGCCATATA-AATG
1 TGATTTGGGCCTAGTGGGCCATATAGAATG
23914 TGA-TTGGGCCTAGTGGGCCATATA
1 TGATTTGGGCCTAGTGGGCCATATA
23938 CAGGTATTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
28 21 0.42
29 28 0.56
30 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (30 bp):
TGATTTGGGCCTAGTGGGCCATATAGAATG
Found at i:26854 original size:16 final size:16
Alignment explanation
Indices: 26833--26865 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
26823 TTGTAACGCC
26833 CCAAAAATCTCGAAAT
1 CCAAAAATCTCGAAAT
26849 CCAAAAATCTCGAAAT
1 CCAAAAATCTCGAAAT
26865 C
1 C
26866 TTGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
CCAAAAATCTCGAAAT
Found at i:28397 original size:28 final size:30
Alignment explanation
Indices: 28323--28406 Score: 129
Period size: 29 Copynumber: 2.9 Consensus size: 30
28313 GAATATAATA
28323 TGATTTGGGCCTAATGGGCCATA-AGAATG
1 TGATTTGGGCCTAATGGGCCATATAGAATG
*
28352 TGATTTGGGCCTAATGGGTCATATA-AATG
1 TGATTTGGGCCTAATGGGCCATATAGAATG
*
28381 TGA-TTGGGCCTAGTGGGCCATATAGA
1 TGATTTGGGCCTAATGGGCCATATAGA
28407 GGTATATGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
28 19 0.38
29 30 0.60
30 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (30 bp):
TGATTTGGGCCTAATGGGCCATATAGAATG
Found at i:34151 original size:39 final size:40
Alignment explanation
Indices: 34040--34223 Score: 182
Period size: 39 Copynumber: 4.7 Consensus size: 40
34030 TCGAATGATA
* * *
34040 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
34080 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * * *
34121 TCCGGGCTAAG-CCCGAAGGCGTTGGAGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
34160 TCCGGGTTAAGTCCCGAAGGCA-TT-TGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
34197 AACTGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
34224 AGGGAGTAGC
Statistics
Matches: 118, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
37 1 0.01
38 28 0.24
39 36 0.31
40 25 0.21
41 27 0.23
42 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:34177 original size:79 final size:79
Alignment explanation
Indices: 34040--34218 Score: 195
Period size: 79 Copynumber: 2.3 Consensus size: 79
34030 TCGAATGATA
* * * *
34040 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCGTTGGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCA-T
34105 TGTGCGAGTTACTAAT
65 T-TGCGAGTTACTAAT
* * **
34121 TCCGGGCTAAG-CCCGAAGGCGTTGGAGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCGTTGGAGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCAT
34183 TTGCGAGTTACT-AT
65 TTGCGAGTTACTAAT
* * *
34197 AACTGGGCTATGTCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGC
34219 ATTTGAGGGA
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
76 2 0.02
77 19 0.23
78 12 0.14
79 26 0.31
80 14 0.17
81 11 0.13
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCGTTGGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TGCGAGTTACTAAT
Found at i:34223 original size:38 final size:38
Alignment explanation
Indices: 34041--34221 Score: 161
Period size: 38 Copynumber: 4.6 Consensus size: 38
34031 CGAATGATAT
* * * *
34041 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGC-ATTGTGC-GAGTTACTA-AA
* *
34082 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* *
34122 CCGGGCTAAG-CCCGAAGGCGTTGGAGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
34160 TCCGGGTTAAGTCCCGAAGGCATT-TGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTA-AA
* *
34199 CTGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
34222 TGAGGGAGTA
Statistics
Matches: 118, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
38 33 0.28
39 33 0.28
40 28 0.24
41 23 0.19
42 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:42417 original size:40 final size:40
Alignment explanation
Indices: 42215--42422 Score: 235
Period size: 40 Copynumber: 5.2 Consensus size: 40
42205 TATTCGAATG
* * *
42215 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
*
42256 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
* *
42296 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGAGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
42335 AAATCTGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
42375 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
42415 ATATCCGG
1 ATATCCGG
42423 TTAAATTCCG
Statistics
Matches: 141, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
39 35 0.25
40 77 0.55
41 28 0.20
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:42425 original size:79 final size:79
Alignment explanation
Indices: 42219--42436 Score: 241
Period size: 79 Copynumber: 2.7 Consensus size: 79
42209 CGAATGATAT
* * * *
42219 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGC-GAGTAG-CTATATCCGG-TTAAGATCCGAAGGCATT
*
42283 TGTGCGAGTTACTAATT
63 TGTGCGAGTTACTAATA
* * *
42300 CCGGGCTAAG-CCCGAAGGCATTGGAGCGAGTTA-CTAAATCTGGGTTAAG-TCCTGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATC-CGGTTAAGATCC-GAAGGCATT
42362 TGTGCGAGTTACT-ATAA
63 TGTGCGAGTTACTAAT-A
*
42379 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGTAGCTATATCCGGTTAA-ATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCCGGTTAAGA-TCCGAAGG
42437 TATGTGATTC
Statistics
Matches: 116, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
78 5 0.04
79 56 0.48
80 45 0.39
81 10 0.09
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCCGGTTAAGATCCGAAGGCATTTGT
GCGAGTTACTAATA
Found at i:44230 original size:42 final size:42
Alignment explanation
Indices: 44161--44264 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
44151 TAAAGGGGTT
* * * * *
44161 TCACACGGCCGATCACATGCCCGTGTCCTTGGCCCGTGTCCC
1 TCACACGGCCGAGCACACGCCCATGTCCTTGGCCCATATCCC
*
44203 TCACACGGTCGAGCACACGCCCATGTCCTTGGCCCATATCCC
1 TCACACGGCCGAGCACACGCCCATGTCCTTGGCCCATATCCC
*
44245 TCACACGGCCTAG-ACACGCC
1 TCACACGGCCGAGCACACGCC
44265 TGTGTCATCG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
41 7 0.13
42 47 0.87
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.18
Consensus pattern (42 bp):
TCACACGGCCGAGCACACGCCCATGTCCTTGGCCCATATCCC
Done.